Biology subjects

Specht, C. D.

Publications and source records attributed to Specht, C. D..

15 recordsLinked to original sources

bioRxiv2026

A Natural-History Study of Reproductive Scaling and Clonality in Co-Occurring Catopsis Griesb

AO_SCPLOWBSTRACTC_SCPLOWMulti-species communities of epiphytic bromeliads are a defining component of Neotropical canopies, yet we have little knowledge of how closely related species differ in the balance struck among vegetative growth, clonal propagation, and sexual reproduction. We compared reproductive output, clonality, and sexual systems in sympatric populations of Catopsis nutans (Sw.) Griseb. and Catopsis sessiliflora (Ruiz & Pav.) Mez occupying citrus groves in central Belize, sampling 235 reproductively mature individuals across 138 host trees in nine groves. Reproductive output, measured as the count of reproductive structures per individual, was modeled with negative binomial generalized linear mixed models that accounted for vegetative size and host tree identity. All sampled C. nutans were hermaphroditic, whereas all C. sessiliflora were unisexual, representing a dioecious population. Reproductive output increased with vegetative size in both species, and the scaling relationship did not differ between them despite their differing sexual systems. After accounting for size, C. sessiliflora produced more reproductive structures and more connected pups than C. nutans, and we found no evidence of a trade-off between clonal and sexual output in both species. Within C. sessiliflora, staminate individuals produced more flowers than pistillate individuals across comparable sizes. Co-occurring Catopsis can differ markedly in baseline reproductive and clonal output while sharing a conserved scaling of output on vegetative size, offering a foundation for further comparisons of sex-specific reproductive allometry in bromeliads.

plant biology↗

bioRxiv2026

Genomic sampling and population structure of farmer-maintained varieties reveal previously uncharacterized diversity of Theobroma cacao L. in Costa Rica

Understanding crop genetic diversity is essential for conservation and breeding, yet farmer-maintained germplasm remains largely underrepresented in genomic studies. Theobroma cacao L. has a complex domestication history and extensive global diversity, and cacao currently cultivated in Central America, particularly in Costa Rica, has been understudied compared to South American and Mexican cultivars despite cultural and historical importance. In this study, we investigate the genetic diversity of cacao from farmer-managed systems across Costa Rica to search for Criollo germplasm and identify and characterize any unique local genetic groups. Ninety-four trees were sampled from 17 farms across four regions of the country and sequenced using whole genome resequencing. Farmer materials were analyzed alongside 166 previously characterized reference accessions representing major cacao genetic groups. Population structure analyses, phylogenetic reconstruction, and network approaches revealed that Costa Rican cacao encompasses multiple known genetic groups, including Criollo-derived lineages, while also harboring locally distinct diversity not fully represented in current global reference collections. Analyses revealed close kinship between many accessions with no clear geographic patterns corresponding to the observed population differentiation, reflecting the effects of farmers in creating dominant patterns of gene flow through seed-saving, clonal propagation, and sharing genotypes among farms. Heterozygosity levels varied substantially among individuals, consistent with a mixture of highly inbred Criollo trees and more heterozygous, admixed genotypes. We find that farmer-managed cacao systems are reservoirs of genetic diversity, including possibly rare or historically important lineages, underscoring the value of these farming systems for effective conservation and management of genomic resources for cacao resilience and improvement.

genomics↗

bioRxiv2025

Diversity of the dwarf palmetto: A phylogeographic analysis of the North American coastal plain and investigation of stem polymorphism in Sabal minor (Jacq.) Pers.

Premise of the studySabal minor is considered one of two cold tolerant palm species, inhabiting riparian zones in temperate and subtropical North America. Ecologically it is often overlooked due to its short compact underground stem that makes it appear stemless, or acaulescent. However, across the central US Gulf Coast S. minor is polymorphic for trunk type, with some individuals identified as caulescent, bearing an above-ground trunk that can reach up to two meters in height. MethodsWe adopt a population genomics approach to characterize the genetic diversity of S. minor and to identify whether the caulescent and acaulescent forms of this temperate palm represent phenotypic variation within a single species. Key resultsThe caulescent and acaulescent forms are not reciprocally monophyletic, suggesting these two forms are phenotypic variants of a single species, S. minor s.l. Genetic clustering does not correspond to stem phenotype but rather reflects five discrete biogeographic clusters that span the native range. These geographic clusters indicate phylogeographic breaks along the Tombigbee River with a history that appears to be influenced by the delta of the Mississippi River. Two ecologically divergent populations, one in White Lake and another in Central Texas, show high genetic differentiation from surrounding populations indicating the presence of ecological barriers to gene flow. ConclusionsPopulation genetic structure of S. minor does not reflect stem morphotype (caulescence or acaulescence) supporting the current taxonomic recognition of one polymorphic species rather than two. However, populations of S. minor show genetic structuring corresponding to known phylogeographic barriers illustrating the dynamic roles regional landscape features played in shaping contemporary S. minor.

evolutionary biology↗

bioRxiv2025

Cytogenetic constraints on hybridization: A meta-analysis investigating the role of chromosome number in monocot hybrid evolution using a newly developed tool, the ploidy deviation index (PDI).

Background and aimsHybridization is a major driver of plant diversity, yet the role of cytogenetic compatibility, particularly differences in chromosome number, remains poorly understood. Differences in parental chromosome number can present barriers to hybrid formation by disrupting meiotic stability, but the extent to which biological and ecological factors influence the chromosomal architecture of hybrids remains poorly quantified, especially in monocots. This study aims to investigate how chromosome number divergence interacts with biological and ecological factors to shape hybrid formation in monocots, using a novel quantitative metric, the Ploidy Deviation Index (PDI), to standardize comparisons of hybrid cytogenetic architecture. Material and methodsWe developed and applied the PDI, a continuous index quantifying chromosome-number deviation between a hybrid and its two parents, across approximately 200 hybrid cases with documented parental karyotypes. Hybrids were categorized as homoploid, uniparentally homoploid, intermediate, or polyploid based on their PDI values. We analyzed the distribution of PDI scores in relation to type of hybrid origin (natural vs. artificial), growth habit, size of the genus (a proxy for richness), and range of chromosome number within a genus (proxy for diversity). Comparisons across categories employed Anderson-Darling k-sample tests, multinomial logistic regression, and Mann-Whitney U tests to determine significance. Key resultsHomoploid hybrids were found to be the most frequent. We found no significant difference in PDI distributions between natural and artificial hybrids. Significant variation in PDI distributions was found among growth habits, with aquatic hybrids more likely to be homoploid and geophytic hybrids showing higher proportions of polyploidy. Intermediate hybrids were common in larger genera with broader chromosome-number ranges, whereas polyploid hybrids showed the highest PDI values in large and karyotypically diverse genera. ConclusionThese results challenge long-held assumptions that polyploidy dominates hybrid formation and reveal that homoploid and intermediate chromosomal configurations are common in monocots. The PDI framework offers a powerful, standardized approach for assessing cytogenetic constraints on hybridization, with implications for systematics, evolutionary biology, and conservation.

plant biology↗

bioRxiv2025

AVITI library prep miniaturization and combining with Illumina data for phylogenomic and population genomic analyses

Recent advancements in next generation sequencing approaches allow for expansion of evolutionary research into the discovery of genetic patterns and processes underlying diversification across scales. The increased popularity of the Element Bioscience AVITI platform, partially due to the high sequencing accuracy and low cost of reagents, is becoming a viable alternative approach for generating massive amounts of comparative sequencing data across diverse organismal lineages. Using a data set of five accessions from the monocot genus Costus, we tested miniaturization conditions for generating robust, cost-effective libraries and made comparisons of data generated by AVITI and Illumina sequencing platforms to investigate the potential for combining data for population genomic and phylogenomic analyses. Our results show that the AVITI and Illumina data sets are highly congruent in terms of inferring overlapping SNPs, with only a small fraction picked up by only one of the two platforms. The rates of duplication in miniaturized libraries were much higher than in full volume libraries and in the Illumina libraries, resulting in missing SNPs and less sequence coverage when volumes are reduced. For all generated libraries, most downstream evolutionary analyses, including clustering algorithms (such as PCA) and phylogenetic inference, yielded similar results. However, Structure analyses were less consistent across datasets, with data from the most miniaturized libraries being assigned to the wrong clusters. The AVITI platform should be seen as a cost-effective approach for generating genomic data for comparison across taxonomic lineages, even for ongoing projects where Illumina data already exists.

evolutionary biology↗

bioRxiv2025

The power to resolve relationships: identifying incongruence and precision of reduced representation and genome-wide data in phylogenomics and population genomics

Target capture of ultraconserved elements (UCEs) and taxon-specific probes are widely used reduced-representation methods in phylogenomics and, increasingly, in population genomics for their ability to retrieve hundreds to thousands of homologous loci across divergent taxa. Meanwhile, declining costs and improved computational methods have made genome resequencing more accessible for non-model species, enabling the generation of datasets that can address evolutionary and ecological questions from micro- to macroevolutionary scales. Whether target capture approaches to likewise generate datasets that can address questions across broad hierarchical scales remains unclear. Here, we assess the efficacy of data collection (i.e., single nucleotide polymorphism (SNP) retention), predicted genetic variation across samples (i.e., heterozygosity), and phylogenetic congruence between data generated using reduced-representation methods and genome resequencing, leveraging publicly available datasets from plants and animals. We found that SNP retention varied by locus type, with genome-wide datasets retaining the highest proportion of SNPs and UCEs the lowest proportion. Heterozygosity also differed, with Benchmarking Universal Single-Copy Orthologs (BUSCOs) producing the lowest estimates, followed by UCEs; the inclusion of supercontig flanking regions raised heterozygosity values moderately. Across all phylogenetic trees, UCE datasets had the lowest bootstrap support, followed by BUSCOs and single copy orthologous genes. Population structure analyses frequently underestimated the number of ancestral populations in reduced-representation datasets, often identifying fewer populations than genome-wide datasets and assigning samples to different clusters. These discrepancies underscore the challenges of relying solely on reduced-representation methods for robust inferences of genetic diversity, phylogenetic relationships, and population structure.

evolutionary biology↗

bioRxiv2025

A revision of the Neotropical Costaceae: results from sixty years of taxonomic struggle

Here we present a taxonomic revision of all neotropical Costaceae represented by 90 species, distributed in four monophyletic genera, Chamaecostus (9 spp.), Costus (76 spp.), Dimerocostus (5 spp.), and Monocostus (1 sp.). The work resulted in three new combinations, several nomenclatural changes, and four insufficiently known species are mentioned to demonstrate the need for continued and ongoing work on this charismatic yet often cryptic lineage of plants. We highlight the seventeen species of Costus and one species of Chamaecostus that were recently described (Maas et al. 2023) based on knowledge that emerged during this complete revisionary work, 60 years in the making. Included in this revision are details concerning the morphology, distribution, ecology, and phylogenetic relationships among the species studied. All currently recognized species are fully described, including notes on taxonomic synonymy, lectotypification, information on distribution and ecology, conservation status (either as evaluated and published in the IUCN Red List of Threatened Species or as estimated for this publication), vernacular names (when given) and short taxonomic notes. For each species, a distribution map is prepared and at least one colour photograph is included to assist in species identification. Dichotomous keys that include all species are provided, as is a list of all (c. 11.000) exsiccatae studied and an index to scientific names.

evolutionary biology↗

bioRxiv2024

Ectopic cambia in Japanese wisteria (Wisteria floribunda) vines are associated with the expression of conserved KNOX genes

Secondary growth is a conserved mechanism that gives rise to vascular tissues produced via a single vascular cambium. Molecular mechanisms underlying this process are characterized mostly in model species bearing typical vascular architecture, while the genetics underlying ecologically-important atypical vascular architectures remain unexplored. We use developmental anatomy, comparative transcriptomics, and molecular evolutionary analyses to address this knowledge gap, investigating how multiple ectopic cambia (EC) form in the woody vine Japanese wisteria. Anatomical studies show EC in Japanese wisteria arise from cortical parenchyma, while cambium-specific transcriptome comparisons reveal that genes acting as regulators of typical cambium development in model species are likewise associated with atypical EC development. Gene trees of KNOX proteins indicate duplication events may contribute to EC formation, including a Fabaceae-specific duplication of KNAT6 detected as under positive selection. These findings reveal insights into the genetics of EC formation, advancing our understanding of the development of complex vascular traits.

plant biology↗

bioRxiv2023

Comparative phylogenomic analyses of SNP versus full locus datasets: insights and recommendations for researchers

PremiseIn phylogenomic analyses, no consensus exists on whether using single nucleotide polymorphisms (SNPs) or including flanking regions (full locus) is best, nor how strictly missing data should be filtered. Moreover, empirical evidence on whether SNP-only trees are suitable for downstream phylogenetic comparative methods such as divergence time estimation and ancestral state reconstructions is lacking. MethodsUsing GBS data from 22 taxa of Glycine, we addressed the effects of SNP vs. locus usage and filtering stringency on phylogenomic inference and phylogenetic comparative methods. We compared branch length, node support, and divergence time estimation across eight datasets with varying amounts of missing data and total size. ResultsOur results reveal five aspects of phylogenomic data usage: 1. tree topology is largely congruent regardless of data type or filtering parameters; 2. filtering missing data too strictly reduces the confidence in some relationships; 3. absolute branch lengths vary by two orders of magnitude between datasets; 4. data type and branch length variation have little effect on divergence time estimation; 5. phylograms significantly alter the estimation of ancestral states. DiscussionWhen conducting phylogenomic analyses we recommend not to filter datasets too strictly to minimize the risk of misleading topologies, low support, and inaccurate divergence times.

evolutionary biology↗

bioRxiv2023

Commonly used Bayesian diversification-rate models produce biologically meaningful differences on empirical phylogenies

Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these shifts may coincide with key evolutionary events such as the development of novel morphological characters, the acquisition of adaptive traits, polyploidization or other structural genomic changes, or dispersal to a new habitat and subsequent increase in environmental niche space. However, while multiple methods now exist to estimate diversification rates and identify shifts using phylogenetic topologies, the appropriate use and accuracy of these methods is hotly debated. Here we test whether five Bayesian methods--Bayesian Analysis of Macroevolutionary Mixtures (BAMM), two implementations of the Lineage-Specific Birth-Death-Shift model (LSBDS and PESTO), the approximate Multi-Type Birth-Death model (MTBD; implemented in BEAST2), and the cladogenetic diversification rate shift model (CLaDS2)--produce comparable results. We apply each of these methods to a set of 65 empirical time-calibrated phylogenies and compare inferences of speciation rate, extinction rate, and net diversification rate. We find that the five methods often infer different speciation, extinction, and net-diversification rates. Consequently, these different estimates may lead to different interpretations of the macroevolutionary dynamics. The different estimates can be attributed to fundamental differences among the compared models. Therefore, the inference of shifts in diver-sification rates is strongly method-dependent. We advise biologists to apply multiple methods to test the robustness of the conclusions or to carefully select the method based on the validity of the underlying model assumptions to their particular empirical system. Lay SummaryUnderstanding why some groups of organisms have more species than others is key to understanding the origin of biodiversity. Theory and empirical evidence suggest that multiple distinct historical events--such as the evolution of particular morphological features (e.g., the flower, the tetrapod limb) and competition amongst species--can produce this pattern of divergent species richness. Identifying when and where on the tree of life shifts in diversification rates occur is important for explaining the origin of modern-day biodiversity and understanding how disparity among species evolves. Several statistical methods have been developed to infer diversification rates and identify these shifts. While these methods each attempt to make inferences about changes in the tempo of diversification, they differ in their underlying statistical models and assumptions. Here we test if these methods draw similar conclusions using a dataset of 65 time-calibrated phylogenies from across multicellular life. We find that inferences of where rate shifts occur strongly depends on the chosen method. Therefore, biologists should choose the model whose assumptions they believe to be the most valid and justify their model choice a priori, or consider using several independent methods to test an evolutionary hypothesis.

evolutionary biology↗

bioRxiv2022

The rapid radiation of Bomarea (Alstroemeriaceae: Liliales), driven by the rise of the Andes

Complex geological events such as mountain uplift affect how, when, and where species originate and go extinct, but measuring those effects is a longstanding challenge. The Andes arose through a series of complex geological processes over the past c. 100 million years, impacting the evolution of regional biota by creating barriers to gene flow, opening up new habitats, and changing local climate patterns. Bomarea are tropical geophytes with ranges extending from central Mexico to central Chile. Of the roughly 120 species of Bomarea, most are found in the Andes, and previous work has suggested that Bomarea diversified rapidly and recently, corresponding with the uplift of the Andes. While many Bomarea species occur over small, isolated ranges, Bomarea edulis occurs significantly beyond the ranges of any other Bomarea species (from central Mexico to northern Argentina) and is thought to have potentially humanmediated dispersal, due to its status as a pre-Columbian food plant. To untangle the potential drivers of diversification and biogeographic history in Bomarea, we used a target-capture approach to sequence nuclear loci of 174 accessions of 124 species, including 16 outgroup species from across the family (Alstroemeriaceae). We included 43 individuals of B. edulis from across its range to assess species monophyly and identify infraspecific phylogeographic patterns. We model biogeographic range evolution in Bomarea and test if Andean orogeny has impacted its diversification. We find that Bomarea originated in the central Andes during the mid-Miocene, then spread north, following the trajectory of major mountain uplift events. Most observed speciation events occurred during the Pleistocene, while global climate cooled and oscillated and the northern Andes achieved their current form. Furthermore, we find that Andean lineages diversified faster than their non-Andean relatives. These results demonstrate a clear macroevolutionary signal of Andean orogeny on this neotropical radiation.

evolutionary biology↗

bioRxiv2021

Unearthing modes of climatic adaptation in underground storage organs across Liliales

Testing adaptive hypotheses about how continuous traits evolve in association with developmentally-structured discrete traits, while accounting for the confounding influence of other, hidden, evolutionary forces, remains a challenge in evolutionary biology. For example, geophytes are herbaceous plants--with underground buds--that use underground storage organs (USOs) to survive extended periods of unfavorable conditions. Such plants have evolved multiple times independently across all major vascular plant lineages. Even within closely related lineages, however, geophytes show impressive variation in the morphological modifications and structures (i.e., "types" of USOs) that allow them to survive underground. Despite the developmental and structural complexity of USOs, the prevailing hypothesis is that they represent convergent evolutionary "solutions" to a common ecological problem, though some recent research has drawn this conclusion into question. We extend existing phylogenetic comparative methods to test for links between the hierarchical discrete morphological traits associated with USOs and adaptation to environmental variables, using a phylogeny of 621 species in Liliales. We found that plants with different USO type do not differ in climatic niche more than expected by chance, with the exception of root morphology, where modified roots are associated with lower temperature seasonality. These findings suggest that root tubers may reflect adaptations to different climatic conditions than those represented by other types of USOs. Thus, the tissue type and developmental origin of the USO structure may influence the way it mediates ecological relationships, which draws into question the appropriateness of ascribing broad ecological patterns uniformly across geophytic taxa. This work provides a new framework for testing adaptive hypotheses and for linking ecological patterns across morphologically varying taxa while accounting for developmental (non-independent) relationships in morphological data. [Macroevolution, geophytes, climatic niche evolution, imperfect correspondence]

evolutionary biology↗

bioRxiv2020

Ancestral class-promiscuity as a driver of functional diversity in the BAHD acyltransferase family in plants

Large enzyme families catalyze metabolic diversification by virtue of their ability to use diverse chemical scaffolds. How enzyme families attain such functional diversity is not clear. Here, we addressed this question using BAHD acyltransferases as a model, and identified the routes by which duplication, promiscuity and sequence changes influenced BAHD diversification. This fast-evolving family expanded drastically during land plant evolution from 1-5 copies in algae to [~]100 copies in diploid angiosperm genomes. In vitro characterization of fourteen BAHDs against a substrate panel and compilation of >160 published activities revealed the wide prevalence of promiscuity among BAHDs. Using phylogenetic analysis, we predicted the substrate classes that the ancestral enzymes were likely capable of using prior to land plant origins. While the anthocyanin acylation activity was fixed in BAHDs later near the origin of angiosperms, in vitro testing of BAHDs from non-seed plant lineages suggested that the ability to acylate anthocyanins likely existed promiscuously millions of years prior to its fixation. Motif enrichment analysis in anthocyanin-acylating BAHDs identified two motifs fixed in the largest anthocyanin acylating clade. Molecular dynamic simulations and enzyme kinetics revealed the important role of an active site tryptophan, whose bulkiness, hydrophobicity and aromaticity are critical for anthocyanin acylation. Our results thus describe the molecular processes in robust, evolvable enzymes that drive emergence of functional diversity in enzyme families. One sentence summaryUsing a combination of phylogenetics, biochemistry and protein structure analysis, we investigated how the BAHD acyltransferase family evolved to use a structurally diverse array of substrates.

plant biology↗

bioRxiv2019

Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation.

Many species from across the vascular plant tree-of-life have modified standard plant tissues into tubers, bulbs, corms, and other underground storage organs (USOs), unique innovations which allow these plants to retreat underground. Our ability to understand the developmental and evolutionary forces that shape these morphologies is limited by a lack of studies on certain USOs and plant clades. Bomarea multiflora (Alstroemeriaceae) is a monocot with tuberous roots, filling a key gap in our understanding of USO development. We take a comparative transcriptomics approach to characterizing the molecular mechanisms of tuberous root formation in B. multiflora and compare these mechanisms to those identified in other USOs across diverse plant lineages. We sequenced transcriptomes from the growing tip of four tissue types (aerial shoot, rhizome, fibrous root, and root tuber) of three individuals of B. multiflora. We identify differentially expressed isoforms between tuberous and non-tuberous roots and test the expression of a priori candidate genes implicated in underground storage in other taxa. We identify 271 genes that are differentially expressed in root tubers versus non-tuberous roots, including genes implicated in cell wall modification, defense response, and starch biosynthesis. We also identify a phosphatidylethanolamine-binding protein (PEBP), which has been implicated in tuberization signalling in other taxa and, through gene-tree analysis, place this copy in a phylogenytic context. These findings suggest that some similar molecular processes underlie the formation of underground storage structures across flowering plants despite the long evolutionary distances among taxa and non-homologous morphologies (e.g., bulbs versus tubers).

plant biology↗

bioRxiv2019

Phylogeny of Paullinia L. (Paullinieae: Sapindaceae), a diverse genus of lianas with rapid fruit evolution

Paullinia L. is a genus of c. 220 mostly Neotropical forest-dwelling lianas that displays a wide diversity of fruit morphologies. Paullinia resembles other members of the Paullinieae in being a climber with stipulate compound leaves and paired inflorescence tendrils. However, it is distinct in having capsular fruits with woody, coriaceous, or crustaceous pericarps. While consistent in this basic plan, the pericarps of Paullinia fruits are otherwise highly variable--in some species they are winged, whereas in others they are without wings or covered with spines. With the exception of the water-dispersed indehiscent spiny fruits of some members of Paullinia sect. Castanella, all species are dehiscent, opening their capsules while they are still attached to the branch, to reveal arillate animal-dispersed seeds. Here we present a molecular phylogeny of Paullinia derived from 11 molecular markers, including nine novel single-copy nuclear markers amplified by microfluidics PCR. This is the first broadly sampled molecular phylogeny for the genus. Paullinia is supported as monophyletic and is sister to Cardiospermum L., which together are sister to Serjania Mill + Urvillea Kunth. We apply this novel phylogenetic hypothesis to test previous infrageneric classifications and to infer that unwinged fruits represent the ancestral condition, from which there were repeated evolutionary transitions and reversals. However, because the seeds of both winged and unwinged fruits are all dispersed by animals, we conclude that the repeated transitions in fruit morphology may relate to visual display strategies to attract animal dispersers, and do not represent transitions to wind dispersal.

evolutionary biology↗