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Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested whether variation in genome and body size is related to morphological variation in the heart and liver using nine species of the salamander genus Plethodon (genome sizes 29-67 gigabases). Our results show that overall organ size is a function of body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force-producing mass and greater intertrabecular space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness may be negligible because low metabolic rates in salamanders relax selective pressure on function of key metabolic organs. Overall, this study suggests large genome and cell size influence the developmental systems involved in heart and liver morphogenesis.

Previous studies demonstrated that nasolacrimal ducts were present in the ancestral plethodontid lineage. Two lineages within Plethodontidae contain individuals that do not possess nasolacrimal ducts: Desmognathus and Eurycea. Earlier works examined only two species of Desmognathus, D. fuscus and D. monticola. We obtained every Desmognathini (Phaeognathus + Desmognathus) species possible from novel collections and museum collections and assessed presence or absence of nasolacrimal ducts using contrast-enhanced computed tomography and routine histological procedures. The goal was to test the hypothesis that nasolacrimal ducts were lost on the evolutionary branch leading to Desmognathus. We rejected our hypothesis by finding that nasolacrimal ducts were absent in all Desmognathus that we examined and Phaeognathus hubrichti; thus, we recovered the absence of nasolacrimal ducts on the evolutionary branch leading to Desmognathini.

Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and changes to anatomy and physiology. Here, we characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome — the caecilian Ichthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models that integrate TE abundance, diversity, and activity, and test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.

Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through its effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested the effects of genome size and body size evolution on heart and liver morphology using nine species of the salamander genus Plethodon (genome sizes 29.3–67 Gb). Our results show that whole organ size is determined by body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force–producing mass and more empty space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness are likely negligible because low metabolic rates in salamanders relax selective pressure on key metabolic organ performance. Overall, this study reveals the effects of large genome and cell size on the developmental systems producing the heart and liver.

The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious species Silene latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 14,126 S. noctiflora genes and 25,317 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Furthermore, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and threefold larger than the 0.9-Gb genome of Silene conica, another species in the same subgenus. Karyotyping confirmed that S. noctiflora is a diploid, indicating that its large genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution.

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation‐related actions., The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, and discordance between gene topologies (e.g., mitonuclear discordance). Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among a confounded species complex of Central American toads.

Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and altered anatomy and physiology. We characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome — the caecilian Ichthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic-recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models integrating TE abundance, diversity, and activity, and we test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.

The angiosperm genusSileneis a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious speciesS. latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts and identify paralogous genes and alternatively spliced genes. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 17,000S. noctifloragenes and 27,000 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Further, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and three-fold larger than the 0.9-Gb genome ofS. conica, another species in the same subgenus. Karyotyping confirmed thatS. noctiflorais a diploid, indicating that its large genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution.

Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary lifecycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships while incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. These high-quality genomic resources capture natural genetic and phenotypic variation across bumblebees, offering new opportunities to advance our understanding of their remarkable ecological success and to identify and manage current and future threats.

Due to their conserved morphology, cryptic species have long been problematic for taxonomists. When attempting to assess diversity and delimit species within these taxa, it has been recognized that an integrative approach can be very useful, whereby independent, yet complementary lines of evidence are utilized. New World microhylids (Anura: Microhylidae: Gastrophryninae) of the genera Gastrophryne and Hypopachus have been highly confounding to taxonomists, due to their extreme morphological conservatism, as well as their fossorial nature resulting in a lack of specimens and public genetic information. Currently, two microhylid species are recognized in Honduras: H. barberi and H. variolosus. Here, we integrate three independent lines of evidence (morphology, osteology, and genetics) to examine previously undescribed diversity among populations of H. barberi in the Lenca Highlands of south-western Honduras. Mitochondrial and nuclear DNA identify populations from the Lenca Highlands as being distinct from other populations previously allocated to H. barberi. This distinction is further supported by divergence dating estimates that place the split between these populations and others of H. barberi in the late-Miocene. We also find several significant morphological and osteological differences between H. barberi and Lenca Highlands populations, including extensively reduced ossification in the (especially cranial) skeleton of the Lenca Highland populations. As a result of these distinctions, we formally describe the Lenca sheep frog as a new species, Hypopachus guancasco sp. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:2B2B4942-2925-42C8-8329-431F55B41AA3

The taxonomy of the diminutive bolitoglossine salamanders of the subgenus Nanotriton has previously been a source of confusion among specialists. At various times, at least three different species of Nanotriton have been reported to occur in Honduras: Bolitoglossa nympha, B. occidentalis and B. rufescens. Phylogenetic analysis of 16S and cyt b from samples from three localities in Honduras (departments of Yoro, Copan and Cortes) confirms that most populations are assignable to B. nympha. Nine samples collected from a single locality on the northern slope of the Sierra de Omoa, between 120 and 190 m in elevation, were found to represent two distinct taxa: B. nympha and B. rufescens. Field examination of these nine specimens found them to be morphologically indistinguishable, including a lack of maxillary teeth in all specimens. As such, in situ identification of the two species in north-western Honduras is problematic given the occurrence of the two taxa in microsympatry in at least one locality. The discovery of yet another divergent lineage of B. rufescens highlights the need for a taxonomic reassessment within this species complex.

We have examined the morphology of the skeletal elements involved in constricted-based tail autotomy in Neotropical plethodontid salamanders of the genus Bolitoglossa. Observed variation in the transverse processes of the first caudal vertebra ranges from a relatively generalized condition, similar to that seen in North American species, to morphologically specialized structures found only in tropical species. Here we present evidence that most species of Bolitoglossa have evolved hypertrophied, reversed transverse processes whose shape and size go beyond what is necessary for structural support in constricted-based tail autotomy and allow the autotomized tail to be used as an anti-predator weapon. We discuss the evolutionary implications of this mechanism.

The diversity of the tropical climbing salamander genus Bolitoglossa (Magnadigita) in Honduras has been underestimated historically, with 11 new species having been described in the past quarter-century. Bolitoglossa celaque is known to occur in three disjunct mountain ranges across the Lenca Highlands region of southwestern Honduras, and previous studies have independently demonstrated differences in mitochondrial genealogy and genome size between populations to the east and west of the Mejocote–San Juan Depression. Sampling from all three mountain ranges represented two genetically distinct clades: one associated with the vicinity of the type locality, Montana de Celaque, and the second consisting of several eastern populations from the departments of Intibuca and La Paz. Distinctiveness of these two clades was further investigated and supported by analyses of morphological variation, geometric morphometrics of foot morphology, and comparative osteology. Based on congruent signals from each line of evidence, we restrict the taxon B. celaque to Montana de Celaque and describe the eastern populations as a new species of Bolitoglossa.

Genome sizes (expressed as C-values, or haploid genome sizes) of six species of Honduran plethodontid salamanders (one species of Nototriton and five of Bolitoglossa) vary greatly. Nototriton has a moderate-sized genome (29.2 pg) relative to other species of salamanders. Genome sizes in the species of Bolitoglossa span a range of 24 pg (∼23.4 gigabases) of DNA and include the largest genomes (83.7 pg) reported for the genus and for the family Plethodontidae. A phylogenetic analysis indicates that genome evolution in this group of salamanders featured mainly large increases in the mass of nuclear DNA. We propose that these evolutionary changes in genome size reflect random drift in small, isolated populations in the highlands of Central America.