Liza J. Conrad

Studies concerning the social behaviours of non-avian reptiles have generally lagged behind other taxa, yet many reptiles are among the most globally threatened animal groups, and their behaviours are key to conservation successes. Herein, we utilized a captive-reared cohort of headstart Gopher Tortoises (Gopherus polyphemus) to test if these animals first discern soil type by social familiarity and/or tortoise exposure and then we tested how social familiarity and sibling status affected social behaviours between individuals. We found that headstart Gopher Tortoises preferentially chose familiar soil over soil that had never been in contact with a Gopher Tortoise, but they also preferred soil that had been in contact with non-familiar individuals over familiar soil. Tortoises displayed the social behaviour of sniffing disproportionately to non-familiar individuals, regardless of sibling status, over familiar individuals. Other social behaviours of nipping, chasing, headbobbing, and colliding were performed independently of social familiarity or sibling status. Taken together, this set of experiments demonstrates that Gopher Tortoises have a high degree of social nuance that is built upon familiarity, and these results could have direct effects on how to optimize headstarting protocols for restoring wild populations.

Understanding the geographic distribution of genetic diversity of imperiled species across all life history stages, and identifying the factors that shape those distributions, are key to maintaining long-term genetic diversity and the health of populations. This knowledge is particularly important for highly mobile marine organisms, whose extensive movements can obscure patterns of population structure. We substantially expand the genetic dataset for the critically endangered hawksbill turtle, Eretmochelys imbricata, in the West Atlantic, focusing on the southwest Caribbean. Our dataset comprises nearly 3,000 mtDNA control region sequences (740 bp) assigned to 60 haplotypes: 41 found in rookeries and 47 in foraging grounds, including 17 orphan haplotypes. The Panama metapopulation represents a major center of genetic diversity for hawksbills, with one of the highest recorded diversity values for the species (h = 0.749, π = 0.00782), nine endemic haplotypes, and four additional haplotypes that are endemic to the Southwest Caribbean. Rarefaction analyses indicate that a sample size of at least 100 is necessary to reveal true haplotype richness at most rookeries. Many-to-many mixed stock analyses, which incorporated rookery size and distance priors for 19 rookeries and 15 developmental foraging grounds, suggest that hatchlings from rookeries in the southwest Caribbean are distributed among multiple, widely-spaced foraging grounds across the West Atlantic. These results support a groups-to-soups analogy, in which genetic variability across foraging grounds represents a continuum of genetic diversity that can best be explained by a “current conveyor” model. The dataset shows that philopatry in hawksbills is not absolute, resulting in true biological dispersal and geneflow on local, regional, and ocean-basin scales, likely facilitated by dispersion during the epipelagic stage. The important contribution of oceanographic features to genetic variation at rookeries and foraging grounds is corroborated, as is the concept of oceanographic “dispersal shadows” that limit geneflow between rookeries. This study reinforces the assertion that all range states share responsibility for the recovery of the hawksbill, because foraging grounds, that are often at distant locations, are the source of future generations of reproductive adults. We also document significant movement by hawksbills between regional management units (RMUs) 29 and 30 in the West Atlantic. The Spanish version of the Abstract is available in Supplementary File 1.

Studies concerning the social behaviours of non-avian reptiles have generally lagged behind other taxa, yet many reptiles are among the most globally threatened animal groups, and their behaviours are key to conservation successes. Herein, we utilized a captive-reared cohort of headstart Gopher Tortoises (Gopherus polyphemus) to test if these animals first discern soil type by social familiarity and/or tortoise exposure and then we tested how social familiarity and sibling status affected social behaviours between individuals. We found that headstart Gopher Tortoises preferentially chose familiar soil over soil that had never been in contact with a Gopher Tortoise, but they also preferred soil that had been in contact with non-familiar individuals over familiar soil. Tortoises displayed the social behaviour of sniffing disproportionately to non-familiar individuals, regardless of sibling status, over familiar individuals. Other social behaviours of nipping, chasing, headbobbing, and colliding were performed independently of social familiarity or sibling status. Taken together, this set of experiments demonstrates that Gopher Tortoises have a high degree of social nuance that is built upon familiarity, and these results could have direct effects on how to optimize headstarting protocols for restoring wild populations.
•Using a cohort of Gopher Tortoises temporarily raised in captivity for conservation, we found that individual tortoises preferentially chose to be on soil from non-familiar tortoises over their own soil and also tortoises avoided soil that had not come into contact with any Gopher Tortoise.•By separating clutch-mates at hatching, we isolated effects of social familiarity from maternal sibling status and found that Gopher Tortoises disproportionately displayed the social behaviour of sniffing non-familiar individuals, regardless of sibling status.•We found that non-familiar sibling pairs did not display any social behaviours differently than non-familiar non-sibling pairs, suggesting that sibling status is not a key social metric that assorts wild Gopher Tortoises into social groups.•Together, these results suggest that Gopher tortoises are both spatially and socially curious yet cautious in both navigating new environments (e.g., novel soil) and interacting with new individuals (e.g., non-familiar members of the same cohort).

Long noncoding RNAs (lncRNAs) have been characterized extensively in animals and are involved in several processes, including homeobox gene expression and X-chromosome inactivation. In comparison, there has been much less detailed characterization of plant lncRNAs, and the number of distinct lncRNAs encoded in plant genomes and their regulation by developmental and epigenetic mechanisms remain largely unknown. Here, we analyzed transcriptome data from Asian rice ( ) and identified 6,309 long intergenic noncoding RNAs (lincRNAs), focusing on their expression in reproductive tissues and organs. Most lincRNAs were expressed in a highly tissue-specific manner, with an unexpectedly high fraction specifically expressed in male gametes. Mutation of a component of the Polycomb Repressive Complex2 (PRC2) resulted in derepression of another large class of lincRNAs, whose expression is correlated with H3K27 trimethylation in developing panicles. Overlap with the sperm cell-specific lincRNAs suggests that epigenetic repression of lincRNAs in the panicles was partially relieved in the male germline. Expression of a subset of lincRNAs also showed modulation by drought in reproductive tissues. Comparison with other cereal genomes showed that the lincRNAs generally have low levels of conservation at both the sequence and structural levels. Use of a novelty detection support vector machine model enabled the detection of nucleotide sequence and structural homology in ∼10% and ∼4% of the lincRNAs in genomes of purple false brome ( ) and maize ( ), respectively. This is the first study to report on a large number of lncRNAs that are targets of repression by PRC2 rather than mediating regulation via PRC2. That the vast majority of the lincRNAs reported here do not overlap with those of other rice studies indicates that these are a significant addition to the known lincRNAs in rice.

The zygotic transition, from a fertilized egg to an embryo, is central to animal and plant reproduction. Animal embryos depend upon maternally provided factors until zygotic genome activation (ZGA). In plants, the timing and parental genome contributions to ZGA are unresolved. Here, we use the flowering plant Oryza sativa (rice) to characterize transcriptomes of time-staged isogenic and hybrid zygotes following fertilization. Large-scale transcriptomic changes were observed in unicellular zygotes, including upregulation of S-phase genes, a characteristic of ZGA. The parental contributions to ZGA were highly asymmetric. Zygotic transcription was primarily from the maternal genome and included genes for basic cellular processes. Transcription of the paternal genome was highly restricted but unexpectedly included genes encoding putative pluripotency factors expressed at the onset of ZGA. Thus, distinct transcriptional activities are exhibited by the parental genomes during the initiation of embryogenesis, which presumptively derive from divergent pre-zygotic transcriptional states established in the gametes.

Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.

Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of lysine 27 of histone H3. The functions of plant PRC2 have been chiefly described in Arabidopsis, but specific functions in other plant species, especially cereals, are still largely unknown. Here we characterize mutants in the rice EMF2B gene, an ortholog of the Arabidopsis EMBRYONIC FLOWER2 (EMF2) gene. Loss of EMF2B in rice results in complete sterility, and mutant flowers have severe floral organ defects and indeterminacy that resemble loss-of-function mutants in E-function floral organ specification genes. Transcriptome analysis identified the E-function genes OsMADS1, OsMADS6 and OsMADS34 as differentially expressed in the emf2b mutant compared with wild type. OsMADS1 and OsMADS6, known to be required for meristem determinacy in rice, have reduced expression in the emf2b mutant, whereas OsMADS34 which interacts genetically with OsMADS1 was ectopically expressed. Chromatin immunoprecipitation for H3K27me3 followed by quantitative (q)RT-PCR showed that all three genes are presumptive targets of PRC2 in the meristem. Therefore, in rice, and possibly other cereals, PRC2 appears to play a major role in floral meristem determinacy through modulation of the expression of E-function genes.

The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, whereas the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells and pollen vegetative cells from Oryza sativa (rice), and identified transcripts for approximately 36000 genes by deep sequencing. The three transcriptomes are highly divergent, with about three-quarters of those genes differentially expressed in the different cell types. Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin. Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle. The sex-specific differences in the expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways. More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions, and their contributions to zygote and seed development.