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Ryvkin A, Furman A, Lebedeva E, Gonotkov M. Analysis of changes in the action potential morphology of the mouse sinoatrial node true pacemaker cells during ontogenetic development in vitro and in silico. Dev Dyn 2024. [PMID: 38459937 DOI: 10.1002/dvdy.701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/31/2024] [Accepted: 02/12/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Maturation of the mouse is accompanied by the increase in heart rate. However, the mechanisms underlying this process remain unclear. We performed an action potentials (APs) recordings in mouse sinoatrial node (SAN) true pacemaker cells and in silico analysis to clarify the mechanisms underlying pre-postnatal period heart rate changes. RESULTS The APs of true pacemaker cells at different stages had similar configurations and dV/dtmax values. The cycle length, action potential duration (APD90 ), maximal diastolic potential (MDP), and AP amplitude decreased, meanwhile the velocity of diastolic depolarization (DDR) increased from E12.5 stage to adult. Using a pharmacological approach we found that in SAN true pacemaker cells ivabradine reduces the DDR and the cycle length significantly stronger in E12.5 than in newborn and adult mice, whereas the effects of Ni2+ and nifedipine were significantly stronger in adult mice. Computer simulations further suggested that the density of the hyperpolarization-activated pacemaker сurrent (If ) decreased during development, whereas transmembrane and intracellular Ca2+ flows increased. CONCLUSIONS The ontogenetic decrease in IK1 density from E12.5 to adult leads to depolarization of MDP to the voltage range in which calcium currents are activated, thereby shifting the balance from the "membrane-clock" to the "calcium-clock."
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Affiliation(s)
| | - Arseniy Furman
- Department of Cardiac Physiology, Institute of Physiology, Komi Science Center, Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Elena Lebedeva
- Department of Cardiac Physiology, Institute of Physiology, Komi Science Center, Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Mikhail Gonotkov
- Department of Cardiac Physiology, Institute of Physiology, Komi Science Center, Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
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2
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Zhang H, Yang P, Liu C, Ma Y, Han Y, Zeng Y, Huang Y, Zhao Y, Zhao Z, He X, E G. Novel Heredity Basis of the Four-Horn Phenotype in Sheep Using Genome-Wide Sequence Data. Animals (Basel) 2023; 13:3166. [PMID: 37893889 PMCID: PMC10603714 DOI: 10.3390/ani13203166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Horns are an important breeding trait for sheep. However, no widely recognized viewpoint on the regulatory genes and mechanisms of horns is available, and the genetic basis of the four-horn phenotype (FHP) is unclear. This work conducted a genome-wide association study with 100 sheep genomes from multiple breeds to investigate the genetic basis of the FHP. The results revealed three significant associations (corrected as p < 1.64 × 10-8) of the InDels (CHR2: g.133,742,709delA, g.133,743,215insC, and g.133,743,940delT) for FHP in the intergenic sequence (IGS) between the MTX2 and the LOC105609047 of CHR2. Moreover, 14 significant associations (corrected as p < 1.42 × 10-9) of SNPs with the FHP phenotype were identified in CHR2 and CHR16, including five (e.g., CHR16: g.40,351,378G > A and g.40,352,577G > A) located in the intron of the ADAMTS12 gene, eight (e.g., CHR2: g.133,727,513C > T and g.133,732,145T > G) in the IGS between MTX2 and LOC105609047, and only one (CHR2: g.133,930,761A > G) in the IGS between HOXD1 and MTX2. Obvious divergence was also observed in genotype patterns between the FHP and others (two horns and hornless) in the HOXD1 and ADAMTS12 gene regions. An extremely significant linkage also occurred between Loci I and Loci II within 100 individuals (LD = -156.02186, p < 0.00001). In summary, our study indicated that the genomic sequences from CHR2 and CHR16 contributed to the FHP in sheep, specifically the key candidate genes HOXD1 and ADAMTS12. These results improved our understanding of the Mendelian genetic basis of the FHP in sheep.
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Affiliation(s)
- Haoyuan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Pu Yang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Chengli Liu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yuehui Ma
- Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Beijing 100097, China
| | - Yanguo Han
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yan Zeng
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yongfu Huang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Zhongquan Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Xiaohong He
- Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Beijing 100097, China
| | - Guangxin E
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
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3
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Swank S, Sanger TJ, Stuart YE. (Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss. Ecol Evol 2021; 11:15484-15497. [PMID: 34824770 PMCID: PMC8601893 DOI: 10.1002/ece3.8226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/31/2021] [Accepted: 09/21/2021] [Indexed: 01/16/2023] Open
Abstract
Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.
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Affiliation(s)
- Samantha Swank
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Thomas J. Sanger
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
| | - Yoel E. Stuart
- Department of BiologyLoyola University ChicagoChicagoIllinoisUSA
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4
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Sadier A, Urban DJ, Anthwal N, Howenstine AO, Sinha I, Sears KE. Making a bat: The developmental basis of bat evolution. Genet Mol Biol 2021; 43:e20190146. [PMID: 33576369 PMCID: PMC7879332 DOI: 10.1590/1678-4685-gmb-2019-0146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/11/2020] [Indexed: 11/28/2022] Open
Abstract
Bats are incredibly diverse, both morphologically and taxonomically. Bats are the only mammalian group to have achieved powered flight, an adaptation that is hypothesized to have allowed them to colonize various and diverse ecological niches. However, the lack of fossils capturing the transition from terrestrial mammal to volant chiropteran has obscured much of our understanding of bat evolution. Over the last 20 years, the emergence of evo-devo in non-model species has started to fill this gap by uncovering some developmental mechanisms at the origin of bat diversification. In this review, we highlight key aspects of studies that have used bats as a model for morphological adaptations, diversification during adaptive radiations, and morphological novelty. To do so, we review current and ongoing studies on bat evolution. We first investigate morphological specialization by reviewing current knowledge about wing and face evolution. Then, we explore the mechanisms behind adaptive diversification in various ecological contexts using vision and dentition. Finally, we highlight the emerging work into morphological novelties using bat wing membranes.
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Affiliation(s)
- Alexa Sadier
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
| | - Daniel J Urban
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA.,American Museum of Natural History, Department of Mammalogy, New York, USA
| | - Neal Anthwal
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
| | - Aidan O Howenstine
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
| | - Ishani Sinha
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
| | - Karen E Sears
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
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5
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Cooper KL. Developmental and Evolutionary Allometry of the Mammalian Limb Skeleton. Integr Comp Biol 2020; 59:1356-1368. [PMID: 31180500 DOI: 10.1093/icb/icz082] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The variety of limb skeletal proportions enables a remarkable diversity of behaviors that include powered flight in bats and flipper-propelled swimming in whales using extremes of a range of homologous limb architectures. Even within human limbs, bone lengths span more than an order of magnitude from the short finger and toe bones to the long arm and leg bones. Yet all of this diversity arises from embryonic skeletal elements that are each a very similar size at formation. In this review article, I survey what is and is not yet known of the development and evolution of skeletal proportion at multiple hierarchical levels of biological organization. These include the cellular parameters of skeletal elongation in the cartilage growth plate, genes associated with differential growth, and putative gene regulatory mechanisms that would allow both covariant and independent evolution of the forelimbs and hindlimbs and of individual limb segments. Although the genetic mechanisms that shape skeletal proportion are still largely unknown, and most of what is known is limited to mammals, it is becoming increasingly apparent that the diversity of bone lengths is an emergent property of a complex system that controls elongation of individual skeletal elements using a genetic toolkit shared by all.
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Affiliation(s)
- Kimberly L Cooper
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093-0377, USA
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6
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Accelerated Evolution of Limb-Related Gene Hoxd11 in the Common Ancestor of Cetaceans and Ruminants (Cetruminantia). G3-GENES GENOMES GENETICS 2020; 10:515-524. [PMID: 31792005 PMCID: PMC7003097 DOI: 10.1534/g3.119.400512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Reduced numbers of carpal and tarsal bones (wrist and ankle joints) are extensively observed in the clade of Cetacea and Ruminantia (Cetruminantia). Homebox D11 (Hoxd11) is one of the important genes required for limb development in mammals. Mutations in Hoxd11 can lead to defects in particular bones of limbs, including carpus and tarsus. To test whether evolutionary changes in Hoxd11 underlie the loss of these bones in Cetruminantia, we sequenced and analyzed Hoxd11 coding sequences and compared them with other 5′ HoxA and HoxD genes in a taxonomic coverage of Cetacea, Ruminantia and other mammalian relatives. Statistical tests on the Hoxd11 sequences found an accelerated evolution in the common ancestor of cetaceans and ruminants, which coincided with the reduction of carpal and tarsal bones in this clade. Five amino acid substitutions (G222S, G227A, G229S, A240T and G261V) and one amino acid deletion (G254Del) occurred in this lineage. In contrast, other 5′ HoxA and HoxD genes do not show this same evolutionary pattern, but instead display a highly conserved pattern of evolution in this lineage. Accelerated evolution of Hoxd11, but not other 5′ HoxA and HoxD genes, is probably related to the reduction of the carpal and tarsal bones in Cetruminantia. Moreover, we found two amino acid substitutions (G110S and D223N) in Hoxd11 that are unique to the lineage of Cetacea, which coincided with hindlimb loss in the common ancestor of cetaceans. Our results give molecular evidence of Hoxd11 adaptive evolution in cetaceans and ruminants, which could be correlated with limb morphological adaptation.
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7
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A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species. Proc Natl Acad Sci U S A 2019; 116:11351-11360. [PMID: 31113885 PMCID: PMC6561249 DOI: 10.1073/pnas.1814995116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
This work represents a large, order-wide evolutionary analysis of the order Chiroptera (bats). Our pipeline for assembling sequence data and curating orthologous multiple sequence alignments includes methods for improving results when combining genomic and transcriptomic data sources. The resulting phylogenetic tree divides the order Chiroptera into Yinpterochiroptera and Yangochiroptera, in disagreement with the previous division into Megachiroptera and Microchiroptera and in agreement with some other recent molecular studies, and also provides evidence for other contested branch placements. We also performed a genome-wide analysis of positive selection and found 181 genes with signatures of positive selection. Enrichment analysis shows these positively selected genes to be primarily related to immune responses but also, surprisingly, collagen formation. Historically, the evolution of bats has been analyzed using a small number of genetic loci for many species or many genetic loci for a few species. Here we present a phylogeny of 18 bat species, each of which is represented in 1,107 orthologous gene alignments used to build the tree. We generated a transcriptome sequence of Hypsignathus monstrosus, the African hammer-headed bat, and additional transcriptome sequence for Rousettus aegyptiacus, the Egyptian fruit bat. We then combined these data with existing genomic and transcriptomic data from 16 other bat species. In the analysis of such datasets, there is no clear consensus on the most reliable computational methods for the curation of quality multiple sequence alignments since these public datasets represent multiple investigators and methods, including different source materials (chromosomal DNA or expressed RNA). Here we lay out a systematic analysis of parameters and produce an advanced pipeline for curating orthologous gene alignments from combined transcriptomic and genomic data, including a software package: the Mismatching Isoform eXon Remover (MIXR). Using this method, we created alignments of 11,677 bat genes, 1,107 of which contain orthologs from all 18 species. Using the orthologous gene alignments created, we assessed bat phylogeny and also performed a holistic analysis of positive selection acting in bat genomes. We found that 181 genes have been subject to positive natural selection. This list is dominated by genes involved in immune responses and genes involved in the production of collagens.
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8
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Usui K, Tokita M. Creating diversity in mammalian facial morphology: a review of potential developmental mechanisms. EvoDevo 2018; 9:15. [PMID: 29946416 PMCID: PMC6003202 DOI: 10.1186/s13227-018-0103-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
Mammals (class Mammalia) have evolved diverse craniofacial morphology to adapt to a wide range of ecological niches. However, the genetic and developmental mechanisms underlying the diversification of mammalian craniofacial morphology remain largely unknown. In this paper, we focus on the facial length and orofacial clefts of mammals and deduce potential mechanisms that produced diversity in mammalian facial morphology. Small-scale changes in facial morphology from the common ancestor, such as slight changes in facial length and the evolution of the midline cleft in some lineages of bats, could be attributed to heterochrony in facial bone ossification. In contrast, large-scale changes of facial morphology from the common ancestor, such as a truncated, widened face as well as the evolution of the bilateral cleft possessed by some bat species, could be brought about by changes in growth and patterning of the facial primordium (the facial processes) at the early stages of embryogenesis.
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Affiliation(s)
- Kaoru Usui
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510 Japan
| | - Masayoshi Tokita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510 Japan
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9
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Sears K, Maier JA, Sadier A, Sorensen D, Urban DJ. Timing the developmental origins of mammalian limb diversity. Genesis 2017; 56. [PMID: 29095555 DOI: 10.1002/dvg.23079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 12/31/2022]
Abstract
Mammals have highly diverse limbs that have contributed to their occupation of almost every niche. Researchers have long been investigating the development of these diverse limbs, with the goals of identifying developmental processes and potential biases that shape mammalian limb diversity. To date, researchers have used techniques ranging from the genomic to the anatomic to investigate the developmental processes shaping the limb morphology of mammals from five orders (Marsupialia, Chiroptera, Rodentia, Cetartiodactyla, and Perissodactyla). Results of these studies suggest that the differential expression of genes controlling diverse cellular processes underlies mammalian limb diversity. Results also suggest that the earliest development of the limb tends to be conserved among mammalian species, while later limb development tends to be more variable. This research has established the mammalian limb as a model system for evolutionary developmental biology, and set the stage for more in-depth, cross-disciplinary research into the genetic controls, tissue-level cellular behaviors, and selective pressures that have driven the developmental evolution of mammalian limbs. Ideally, these studies will be performed in a diverse suite of mammalian species within a comparative, phylogenetic framework.
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Affiliation(s)
- Karen Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, 90095
| | - Jennifer A Maier
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, 90095
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, 90095
| | - Daniel Sorensen
- Lillehei Heart Institute, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Daniel J Urban
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, 90095.,Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801.,Department of Mammalogy, American Museum of Natural History, New York, New York, 10024
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10
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Cooper LN, Sears KE, Armfield BA, Kala B, Hubler M, Thewissen JGM. Review and experimental evaluation of the embryonic development and evolutionary history of flipper development and hyperphalangy in dolphins (Cetacea: Mammalia). Genesis 2017; 56. [DOI: 10.1002/dvg.23076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 09/27/2017] [Accepted: 09/29/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Lisa Noelle Cooper
- Department of Anatomy and NeurobiologyNEOMEDRootstown OH44272‐0095
- Department of Anatomy and NeurobiologyMusculoskeletal Biology Research Group at NEOMEDRootstown OH44272‐0095
| | - Karen E. Sears
- Department of Animal BiologyUniversity of IllinoisUrbana IL61801
- University of Illinois, Institute for Genomic BiologyUrbana IL61801
| | - Brooke A. Armfield
- Molecular Genetics and MicrobiologyUniversity of FloridaGainesville FL32610
| | - Bhavneet Kala
- Department of Anatomy and NeurobiologyNEOMEDRootstown OH44272‐0095
| | - Merla Hubler
- Department of Animal BiologyUniversity of IllinoisUrbana IL61801
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11
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Maier JA, Rivas-Astroza M, Deng J, Dowling A, Oboikovitz P, Cao X, Behringer RR, Cretekos CJ, Rasweiler JJ, Zhong S, Sears KE. Transcriptomic insights into the genetic basis of mammalian limb diversity. BMC Evol Biol 2017; 17:86. [PMID: 28335721 PMCID: PMC5364624 DOI: 10.1186/s12862-017-0902-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 02/03/2017] [Indexed: 12/28/2022] Open
Abstract
Background From bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species. Results We assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species. Conclusions Taken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0902-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer A Maier
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jenny Deng
- Department of Genetics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Anna Dowling
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Paige Oboikovitz
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - Xiaoyi Cao
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Chris J Cretekos
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209, USA
| | - John J Rasweiler
- Department of Obstetrics and Gynecology, State University Downstate Medical Center, 450 Clarkson, Avenue, Brooklyn, NY, 11203, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Karen E Sears
- School of Integrative Biology, University of Illinois, 505 S Goodwin Avenue, Urbana, IL, 61801, USA. .,Institute for Genomic Biology, University of Illinois, 1206 W Gregory Drive, Urbana, IL, 61801, USA.
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12
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Abstract
The limb is a commonly used model system for developmental biology. Given the need for precise control of complex signalling pathways to achieve proper patterning, the limb is also becoming a model system for gene regulation studies. Recent developments in genomic technologies have enabled the genome-wide identification of regulatory elements that control limb development, yielding insights into the determination of limb morphology and forelimb versus hindlimb identity. The modulation of regulatory interactions - for example, through the modification of regulatory sequences or chromatin architecture - can lead to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.
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Affiliation(s)
- Florence Petit
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,University of Lille, CHU Lille, EA 7364-RADEME, F-59000 Lille, France
| | - Karen E Sears
- School of Integrative Biology, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,Institute for Human Genetics, University of California San Francisco, California 94158, USA
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13
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Saxena A, Towers M, Cooper KL. The origins, scaling and loss of tetrapod digits. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0482. [PMID: 27994123 PMCID: PMC5182414 DOI: 10.1098/rstb.2015.0482] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/19/2022] Open
Abstract
Many of the great morphologists of the nineteenth century marvelled at similarities between the limbs of diverse species, and Charles Darwin noted these homologies as significant supporting evidence for descent with modification from a common ancestor. Sir Richard Owen also took great care to highlight each of the elements of the forelimb and hindlimb in a multitude of species with focused attention on the homology between the hoof of the horse and the middle digit of man. The ensuing decades brought about a convergence of palaeontology, experimental embryology and molecular biology to lend further support to the homologies of tetrapod limbs and their developmental origins. However, for all that we now understand about the conserved mechanisms of limb development and the development of gross morphological disturbances, little of what is presented in the experimental or medical literature reflects the remarkable diversity resulting from the 450 million year experiment of natural selection. An understanding of conserved and divergent limb morphologies in this new age of genomics and genome engineering promises to reveal more of the developmental potential residing in all limbs and to unravel the mechanisms of evolutionary variation in limb size and shape. In this review, we present the current state of our rapidly advancing understanding of the evolutionary origin of hands and feet and highlight what is known about the mechanisms that shape diverse limbs.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew Towers
- Bateson Centre, Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Kimberly L. Cooper
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,e-mail:
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14
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Ball H, Moussa F, Mbimba T, Orman R, Safadi F, Cooper L. Methods and insights from the characterization of osteoprogenitor cells of bats (Mammalia: Chiroptera). Stem Cell Res 2016; 17:54-61. [DOI: 10.1016/j.scr.2016.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 01/14/2023] Open
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15
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Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N. Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PLoS Genet 2016; 12:e1005738. [PMID: 27019019 PMCID: PMC4809552 DOI: 10.1371/journal.pgen.1005738] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/23/2015] [Indexed: 02/06/2023] Open
Abstract
The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor, but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs) that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing.
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Affiliation(s)
- Betty M. Booker
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Tara Friedrich
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Gladstone Institutes, San Francisco, California, United States of America
| | - Mandy K. Mason
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Julia E. VanderMeer
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Key Laboratory of Advanced Control and Optimization for Chemical Processes of the Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Walter L. Eckalbar
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Malcolm Logan
- Division of Developmental Biology, MRC-National Institute for Medical Research, Mill Hill, London, United Kingdom
- Randall Division of Cell and Molecular Biophysics, King’s College London, Guys Campus, London, United Kingdom
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Katherine S. Pollard
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Gladstone Institutes, San Francisco, California, United States of America
- Division of Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (KSP); (NA)
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (KSP); (NA)
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Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM, Nishizaki S, Muswamba-Nday C, Terhune E, Nevonen KA, Makki N, Friedrich T, VanderMeer JE, Pollard KS, Carbone L, Wall JD, Illing N, Ahituv N. Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet 2016; 48:528-36. [PMID: 27019111 PMCID: PMC4848140 DOI: 10.1038/ng.3537] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 03/04/2016] [Indexed: 12/21/2022]
Abstract
Bats are the only mammals capable of powered flight, but little is known about the genetic determinants that shape their wings. Here we generated a genome for Miniopterus natalensis and performed RNA-seq and ChIP-seq (H3K27ac and H3K27me3) analyses on its developing forelimb and hindlimb autopods at sequential embryonic stages to decipher the molecular events that underlie bat wing development. Over 7,000 genes and several long noncoding RNAs, including Tbx5-as1 and Hottip, were differentially expressed between forelimb and hindlimb, and across different stages. ChIP-seq analysis identified thousands of regions that are differentially modified in forelimb and hindlimb. Comparative genomics found 2,796 bat-accelerated regions within H3K27ac peaks, several of which cluster near limb-associated genes. Pathway analyses highlighted multiple ribosomal proteins and known limb patterning signaling pathways as differentially regulated and implicated increased forelimb mesenchymal condensation in differential growth. In combination, our work outlines multiple genetic components that likely contribute to bat wing formation, providing insights into this morphological innovation.
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Affiliation(s)
- Walter L Eckalbar
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Stephen A Schlebusch
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Mandy K Mason
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Zoe Gill
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Ash V Parker
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Betty M Booker
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Sierra Nishizaki
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | | | - Elizabeth Terhune
- Oregon National Primate Research Center, Division of Neuroscience, Primate Genetics Section, Beaverton, Oregon, USA.,Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Kimberly A Nevonen
- Oregon National Primate Research Center, Division of Neuroscience, Primate Genetics Section, Beaverton, Oregon, USA
| | - Nadja Makki
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Tara Friedrich
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.,Gladstone Institutes, San Francisco, California, USA
| | - Julia E VanderMeer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.,Gladstone Institutes, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Lucia Carbone
- Oregon National Primate Research Center, Division of Neuroscience, Primate Genetics Section, Beaverton, Oregon, USA.,Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon, USA
| | - Jeff D Wall
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
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18
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Martínez-Abadías N, Mateu R, Niksic M, Russo L, Sharpe J. Geometric Morphometrics on Gene Expression Patterns Within Phenotypes: A Case Example on Limb Development. Syst Biol 2015; 65:194-211. [PMID: 26377442 PMCID: PMC4748747 DOI: 10.1093/sysbio/syv067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/11/2015] [Indexed: 01/12/2023] Open
Abstract
How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are associated with changes in morphology using the limb as a case example. Our method combines molecular biology techniques, such as whole-mount in situ hybridization, with image and shape analysis, extending the use of Geometric Morphometrics to the analysis of nonanatomical shapes, such as gene expression domains. Elliptical Fourier and Procrustes-based semilandmark analyses were used to analyze the variation and covariation patterns of the limb bud shape with the expression patterns of two relevant genes for limb morphogenesis, Hoxa11 and Hoxa13. We devised a multiple thresholding method to semiautomatically segment gene domains at several expression levels in large samples of limb buds from C57Bl6 mouse embryos between 10 and 12 postfertilization days. Besides providing an accurate phenotyping tool to quantify the spatiotemporal dynamics of gene expression patterns within developing structures, our morphometric analyses revealed high, non-random, and gene-specific variation undergoing canalization during limb development. Our results demonstrate that Hoxa11 and Hoxa13, despite being paralogs with analogous functions in limb patterning, show clearly distinct dynamic patterns, both in shape and size, and are associated differently with the limb bud shape. The correspondence between our results and already well-established molecular processes underlying limb development confirms that this morphometric approach is a powerful tool to extract features of development regulating morphogenesis. Such multilevel analyses are promising in systems where not so much molecular information is available and will advance our understanding of the genotype–phenotype map. In systematics, this knowledge will increase our ability to infer how evolution modified a common developmental pattern to generate a wide diversity of morphologies, as in the vertebrate limb.
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Affiliation(s)
- Neus Martínez-Abadías
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roger Mateu
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Martina Niksic
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lucia Russo
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Sharpe
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Mason MK, Hockman D, Curry L, Cunningham TJ, Duester G, Logan M, Jacobs DS, Illing N. Retinoic acid-independent expression of Meis2 during autopod patterning in the developing bat and mouse limb. EvoDevo 2015; 6:6. [PMID: 25861444 PMCID: PMC4389300 DOI: 10.1186/s13227-015-0001-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 02/04/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The bat has strikingly divergent forelimbs (long digits supporting wing membranes) and hindlimbs (short, typically free digits) due to the distinct requirements of both aerial and terrestrial locomotion. During embryonic development, the morphology of the bat forelimb deviates dramatically from the mouse and chick, offering an alternative paradigm for identifying genes that play an important role in limb patterning. RESULTS Using transcriptome analysis of developing Natal long-fingered bat (Miniopterus natalensis) fore- and hindlimbs, we demonstrate that the transcription factor Meis2 has a significantly higher expression in bat forelimb autopods compared to hindlimbs. Validation by reverse transcriptase and quantitative polymerase chain reaction (RT-qPCR) and whole mount in situ hybridisation shows that Meis2, conventionally known as a marker of the early proximal limb bud, is upregulated in the bat forelimb autopod from CS16. Meis2 expression is localised to the expanding interdigital webbing and the membranes linking the wing to the hindlimb and tail. In mice, Meis2 is also expressed in the interdigital region prior to tissue regression. This interdigital Meis2 expression is not activated by retinoic acid (RA) signalling as it is present in the retained interdigital tissue of Rdh10 (trex/trex) mice, which lack RA. Additionally, genes encoding RA-synthesising enzymes, Rdh10 and Aldh1a2, and the RA nuclear receptor Rarβ are robustly expressed in bat fore- and hindlimb interdigital tissues indicating that the mechanism that retains interdigital tissue in bats also occurs independently of RA signalling. CONCLUSIONS Mammalian interdigital Meis2 expression, and upregulation in the interdigital webbing of bat wings, suggests an important role for Meis2 in autopod development. Interdigital Meis2 expression is RA-independent, and retention of interdigital webbing in bat wings is not due to the suppression of RA-induced cell death. Rather, RA signalling may play a role in the thinning (rather than complete loss) of the interdigital tissue in the bat forelimb, while Meis2 may interact with other factors during both bat and mouse autopod development to maintain a pool of interdigital cells that contribute to digit patterning and growth.
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Affiliation(s)
- Mandy K Mason
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 South Africa
| | - Dorit Hockman
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 South Africa ; Present address: Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS UK
| | - Lyle Curry
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 South Africa
| | - Thomas J Cunningham
- Sanford-Burnham Medical Research Institute, Development, Aging, and Regeneration Program, La Jolla, 92037 California USA
| | - Gregg Duester
- Sanford-Burnham Medical Research Institute, Development, Aging, and Regeneration Program, La Jolla, 92037 California USA
| | - Malcolm Logan
- Randall Division, King's College London, London, SE1 1UL UK
| | - David S Jacobs
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7701 South Africa
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 South Africa
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20
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Tokita M. How the pterosaur got its wings. Biol Rev Camb Philos Soc 2014; 90:1163-78. [PMID: 25361444 DOI: 10.1111/brv.12150] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/10/2014] [Accepted: 10/01/2014] [Indexed: 12/19/2022]
Abstract
Throughout the evolutionary history of life, only three vertebrate lineages took to the air by acquiring a body plan suitable for powered flight: birds, bats, and pterosaurs. Because pterosaurs were the earliest vertebrate lineage capable of powered flight and included the largest volant animal in the history of the earth, understanding how they evolved their flight apparatus, the wing, is an important issue in evolutionary biology. Herein, I speculate on the potential basis of pterosaur wing evolution using recent advances in the developmental biology of flying and non-flying vertebrates. The most significant morphological features of pterosaur wings are: (i) a disproportionately elongated fourth finger, and (ii) a wing membrane called the brachiopatagium, which stretches from the posterior surface of the arm and elongated fourth finger to the anterior surface of the leg. At limb-forming stages of pterosaur embryos, the zone of polarizing activity (ZPA) cells, from which the fourth finger eventually differentiates, could up-regulate, restrict, and prolong expression of 5'-located Homeobox D (Hoxd) genes (e.g. Hoxd11, Hoxd12, and Hoxd13) around the ZPA through pterosaur-specific exploitation of sonic hedgehog (SHH) signalling. 5'Hoxd genes could then influence downstream bone morphogenetic protein (BMP) signalling to facilitate chondrocyte proliferation in long bones. Potential expression of Fgf10 and Tbx3 in the primordium of the brachiopatagium formed posterior to the forelimb bud might also facilitate elongation of the phalanges of the fourth finger. To establish the flight-adapted musculoskeletal morphology shared by all volant vertebrates, pterosaurs probably underwent regulatory changes in the expression of genes controlling forelimb and pectoral girdle musculoskeletal development (e.g. Tbx5), as well as certain changes in the mode of cell-cell interactions between muscular and connective tissues in the early phase of their evolution. Developmental data now accumulating for extant vertebrate taxa could be helpful in understanding the cellular and molecular mechanisms of body-plan evolution in extinct vertebrates as well as extant vertebrates with unique morphology whose embryonic materials are hard to obtain.
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Affiliation(s)
- Masayoshi Tokita
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, U.S.A
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Dai M, Wang Y, Fang L, Irwin DM, Zhu T, Zhang J, Zhang S, Wang Z. Differential expression of Meis2, Mab21l2 and Tbx3 during limb development associated with diversification of limb morphology in mammals. PLoS One 2014; 9:e106100. [PMID: 25166052 PMCID: PMC4148388 DOI: 10.1371/journal.pone.0106100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 07/27/2014] [Indexed: 11/19/2022] Open
Abstract
Bats are the only mammals capable of self-powered flight using wings. Differing from mouse or human limbs, four elongated digits within a broad wing membrane support the bat wing, and the foot of the bat has evolved a long calcar that spread the interfemoral membrane. Our recent mRNA sequencing (mRNA-Seq) study found unique expression patterns for genes at the 5' end of the Hoxd gene cluster and for Tbx3 that are associated with digit elongation and wing membrane growth in bats. In this study, we focused on two additional genes, Meis2 and Mab21l2, identified from the mRNA-Seq data. Using whole-mount in situ hybridization (WISH) we validated the mRNA-Seq results for differences in the expression patterns of Meis2 and Mab21l2 between bat and mouse limbs, and further characterize the timing and location of the expression of these two genes. These analyses suggest that Meis2 may function in wing membrane growth and Mab21l2 may have a role in AP and DV axial patterning. In addition, we found that Tbx3 is uniquely expressed in the unique calcar structure found in the bat hindlimb, suggesting a role for this gene in calcar growth and elongation. Moreover, analysis of the coding sequences for Meis2, Mab21l2 and Tbx3 showed that Meis2 and Mab21l2 have high sequence identity, consistent with the functions of genes being conserved, but that Tbx3 showed accelerated evolution in bats. However, evidence for positive selection in Tbx3 was not found, which would suggest that the function of this gene has not been changed. Together, our findings support the hypothesis that the modulation of the spatiotemporal expression patterns of multiple functional conserved genes control limb morphology and drive morphological change in the diversification of mammalian limbs.
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Affiliation(s)
- Mengyao Dai
- Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai, China
| | - Yao Wang
- Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai, China
| | - Lu Fang
- Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Tengteng Zhu
- Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai, China
| | - Junpeng Zhang
- Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai, China
| | - Shuyi Zhang
- Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai, China
| | - Zhe Wang
- Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai, China
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