M. Brent Hawkins
@homeobox.bsky.social
Developmental genetics and evolution of the vertebrate skeleton. Postdoc in the Harris Lab at Boston Children's Hospital/Harvard Medical School. Every day is fin day. He/him/his.
This is Hilma af Klint coded Esoteric Knowledge
October 10, 2025 at 1:38 AM
This is Hilma af Klint coded Esoteric Knowledge
Last Friday I was hosted by @phernandez.bsky.social @evolvwing.bsky.social to give departmental seminar at GWU Biology. Exciting to hear about the great evo-devo being done there by wonderful people in a beautiful city. And future collaborations!Thank you for having me!
September 15, 2025 at 5:15 PM
Last Friday I was hosted by @phernandez.bsky.social @evolvwing.bsky.social to give departmental seminar at GWU Biology. Exciting to hear about the great evo-devo being done there by wonderful people in a beautiful city. And future collaborations!Thank you for having me!
Myomeres in the sky
July 18, 2025 at 9:14 PM
Myomeres in the sky
True loaches also exhibit modifications to the dorsal aspect of the pectoral fin, and males develop large ornaments on the fin rays that exhibit species-specific morphology. They also develop dorsal hook-like flanges in the posterior fin region.
July 7, 2025 at 6:47 AM
True loaches also exhibit modifications to the dorsal aspect of the pectoral fin, and males develop large ornaments on the fin rays that exhibit species-specific morphology. They also develop dorsal hook-like flanges in the posterior fin region.
Additionally, we also detected accelerated sequence evolution within the LARM2 element in the lineage leading to the hillstream loaches as well as the true loaches (family Cobitidae).
July 7, 2025 at 6:47 AM
Additionally, we also detected accelerated sequence evolution within the LARM2 element in the lineage leading to the hillstream loaches as well as the true loaches (family Cobitidae).
However, we detected a deletion specifically within the hillstream loach lineage in the LARM1x element. This deleted region is predicted to contain transcription factor binding sites and its removal could impact Lmx1b regulation
July 7, 2025 at 6:47 AM
However, we detected a deletion specifically within the hillstream loach lineage in the LARM1x element. This deleted region is predicted to contain transcription factor binding sites and its removal could impact Lmx1b regulation
We asked if the hillstream loach lineage exhibited variation in the LARM architecture that correlated with apparent modification of DV pattern. Genomic alignments revealed that the various LARM elements are largely conserved across the cypriniforms, which include zfish & the loaches amongst others
July 7, 2025 at 6:47 AM
We asked if the hillstream loach lineage exhibited variation in the LARM architecture that correlated with apparent modification of DV pattern. Genomic alignments revealed that the various LARM elements are largely conserved across the cypriniforms, which include zfish & the loaches amongst others
Using microCT datasets from Morphosource, we found that hillstream loaches naturally develop the ectopic dorsal flanges we observe in holo-LARM deletion mutant fins. This phenocopy is a derived condition, as most cypriniform fishes have a configuration similar to WT zfish with ventral flanges only
July 7, 2025 at 6:47 AM
Using microCT datasets from Morphosource, we found that hillstream loaches naturally develop the ectopic dorsal flanges we observe in holo-LARM deletion mutant fins. This phenocopy is a derived condition, as most cypriniform fishes have a configuration similar to WT zfish with ventral flanges only
We discovered that hillstream loaches have modified the DV axis of the pectoral fin in ways that facilitate an adaptive mode of locomotion. These fishes have a depressed body and expanded fins that enable them to adhere to surfaces in fast flowing water and even climb up waterfalls
July 7, 2025 at 6:47 AM
We discovered that hillstream loaches have modified the DV axis of the pectoral fin in ways that facilitate an adaptive mode of locomotion. These fishes have a depressed body and expanded fins that enable them to adhere to surfaces in fast flowing water and even climb up waterfalls
However, expression persists in the median fins of these mutants demonstrating that the paired fin regulatory program differs from the median fins. In contrast to other programs, we propose that LARM-mediated Lmx1b expression is a regulatory novelty that arose specifically in the paired appendages
July 7, 2025 at 6:47 AM
However, expression persists in the median fins of these mutants demonstrating that the paired fin regulatory program differs from the median fins. In contrast to other programs, we propose that LARM-mediated Lmx1b expression is a regulatory novelty that arose specifically in the paired appendages
If paired fin DV patterning arose from the redeployment of median fin Lmx1b programs, then we would expect that the LARM is required for Lmx1b expression in both types of fins. We observed that Lmx1b expression is lost from the pectoral fin buds of holo-LARM deletion animals.
July 7, 2025 at 6:47 AM
If paired fin DV patterning arose from the redeployment of median fin Lmx1b programs, then we would expect that the LARM is required for Lmx1b expression in both types of fins. We observed that Lmx1b expression is lost from the pectoral fin buds of holo-LARM deletion animals.
We found that lamprey ammocete larvae express Lmx1b in the posterior median fin, just like in gnathostomes, suggesting this is an ancestral feature with an ancient origin that is shared across both jawed and jawless vertebrates
July 7, 2025 at 6:47 AM
We found that lamprey ammocete larvae express Lmx1b in the posterior median fin, just like in gnathostomes, suggesting this is an ancestral feature with an ancient origin that is shared across both jawed and jawless vertebrates
In the mutant animals we found that the tendons attach directly to the ectopic dorsal flanges in proximal fin regions, while in WT animals the tendons would normally have a more distal attachment. These changes in the musculoskeletal system modify how the fin can be moved & echo the mouse phenotype
July 7, 2025 at 6:47 AM
In the mutant animals we found that the tendons attach directly to the ectopic dorsal flanges in proximal fin regions, while in WT animals the tendons would normally have a more distal attachment. These changes in the musculoskeletal system modify how the fin can be moved & echo the mouse phenotype
We also observed changes in how the skeleton is integrated with the musculature when the holo-LARM is removed. Using whole-mount clearing and immunolabelling with confocal microscopy, we found consistent integrated changes in the tendonous attachments to the bony fin rays
July 7, 2025 at 6:47 AM
We also observed changes in how the skeleton is integrated with the musculature when the holo-LARM is removed. Using whole-mount clearing and immunolabelling with confocal microscopy, we found consistent integrated changes in the tendonous attachments to the bony fin rays
Normal zebrafish males develop keratinized breeding tubercles on the dorsal (but not ventral) pectoral fin surface. We found that holo-LARM mutant males no longer develop these structures, consistent with a transversion to ventral identity in the integument
July 7, 2025 at 6:47 AM
Normal zebrafish males develop keratinized breeding tubercles on the dorsal (but not ventral) pectoral fin surface. We found that holo-LARM mutant males no longer develop these structures, consistent with a transversion to ventral identity in the integument
This larger deletion recapitulated the Lmx1b null double-ventral phenotype while retaining viability in the mutants, just like the mouse LARM1/2 deletion. Using this holo-LARM deletion line we were able to assess impacts on DV patterning beyond the bony flanges.
July 7, 2025 at 6:47 AM
This larger deletion recapitulated the Lmx1b null double-ventral phenotype while retaining viability in the mutants, just like the mouse LARM1/2 deletion. Using this holo-LARM deletion line we were able to assess impacts on DV patterning beyond the bony flanges.
We also inspected ATACseq data sets & found peaks of open chromatin which coincided with the LARM2 hits from our Holostean Bridge alignments. To test if this expanded interval contained the LARM regulatory information we made a larger ~7 kb LARM deletion in the zebrafish encompassing LARM1 and LARM2
July 7, 2025 at 6:47 AM
We also inspected ATACseq data sets & found peaks of open chromatin which coincided with the LARM2 hits from our Holostean Bridge alignments. To test if this expanded interval contained the LARM regulatory information we made a larger ~7 kb LARM deletion in the zebrafish encompassing LARM1 and LARM2
To find zfish LARM elements we missed, we used the Holostean Bridge approach by aligning the mouse and zfish genomes to gar. Pairwise alignments to gar pointed to a putative LARM2 element in the zfish which our first model initially missed.
July 7, 2025 at 6:47 AM
To find zfish LARM elements we missed, we used the Holostean Bridge approach by aligning the mouse and zfish genomes to gar. Pairwise alignments to gar pointed to a putative LARM2 element in the zfish which our first model initially missed.
When we used CRIPSR to remove the 164 bp element from the zebrafish genome, and we saw no change in phenotype, indicating that is it not necessary for dorsal pectoral fin Lmx1b expression. However, we know Lmx1b protein function IS required for dorsality. Could there be cryptic zfish LARM elements?
July 7, 2025 at 6:47 AM
When we used CRIPSR to remove the 164 bp element from the zebrafish genome, and we saw no change in phenotype, indicating that is it not necessary for dorsal pectoral fin Lmx1b expression. However, we know Lmx1b protein function IS required for dorsality. Could there be cryptic zfish LARM elements?
However, when two copies of the zfish 164 bp element were included in addition to the intact mouse LARM we observed an Lmx1b gain-of-function, with mice now showing a double-dorsal phenotype. This suggests that the zfish LARM1s element can function as an enhancer depending on genomic context.
July 7, 2025 at 6:47 AM
However, when two copies of the zfish 164 bp element were included in addition to the intact mouse LARM we observed an Lmx1b gain-of-function, with mice now showing a double-dorsal phenotype. This suggests that the zfish LARM1s element can function as an enhancer depending on genomic context.
When the mouse LARM was replaced with the 164 bp zfish LARM1s element, the limbs showed the same phenotype as the full LARM1 + LARM2 knockout, meaning the small zfish piece cannot compensate for the full mouse LARM and is not sufficient to drive dorsal fates.
July 7, 2025 at 6:47 AM
When the mouse LARM was replaced with the 164 bp zfish LARM1s element, the limbs showed the same phenotype as the full LARM1 + LARM2 knockout, meaning the small zfish piece cannot compensate for the full mouse LARM and is not sufficient to drive dorsal fates.
Using transgenic assays in zebrafish, we found that LARM orthologs from across gnathostome evolution are able to drive reporter gene expression in the fins of zebrafish embryos, demonstrating functional conservation of appendage regulation of Lmx1b.
July 7, 2025 at 6:47 AM
Using transgenic assays in zebrafish, we found that LARM orthologs from across gnathostome evolution are able to drive reporter gene expression in the fins of zebrafish embryos, demonstrating functional conservation of appendage regulation of Lmx1b.
To identify the LARM element outside of tetrapods, we made a bioinformatic model to search vertebrate genomes for similar motifs. We identified LARM elements in all major vertebrate lineages except the cyclostomes, which lack paired fins. Thus, LARM seems to be a jawed vertebrate-specific feature.
July 7, 2025 at 6:47 AM
To identify the LARM element outside of tetrapods, we made a bioinformatic model to search vertebrate genomes for similar motifs. We identified LARM elements in all major vertebrate lineages except the cyclostomes, which lack paired fins. Thus, LARM seems to be a jawed vertebrate-specific feature.
Next we asked if dorsal appendage Lmx1b expression is controlled in fins and limbs by conserved non-coding regulatory elements. In mice, this gene expression is controlled by the LARM elements, & removal of the LARM recapitulates the Lmx1b null phenotype while retaining viability (Haro et al., 2021)
July 7, 2025 at 6:47 AM
Next we asked if dorsal appendage Lmx1b expression is controlled in fins and limbs by conserved non-coding regulatory elements. In mice, this gene expression is controlled by the LARM elements, & removal of the LARM recapitulates the Lmx1b null phenotype while retaining viability (Haro et al., 2021)
This change in fin anatomy is analogous to what happens when Lmx1b function is removed in limbs. Mice homozygous for Lmx1b have paws w/ mirrored double-ventral form, developing ventral pads on both sides and losing the nail (Chen et al., 1998). Lmx1b null mice & zfish are inviable past early life.
July 7, 2025 at 6:47 AM
This change in fin anatomy is analogous to what happens when Lmx1b function is removed in limbs. Mice homozygous for Lmx1b have paws w/ mirrored double-ventral form, developing ventral pads on both sides and losing the nail (Chen et al., 1998). Lmx1b null mice & zfish are inviable past early life.