Biology subjects

Ballen, G. A.

Publications and source records attributed to Ballen, G. A..

10 recordsLinked to original sources

bioRxiv2026

Acrean fish diversity back in time: Paleoichthyology of the Rio Acre fossil fauna in Brazil

Freshwater fishes are an important component of the Neogene fossil record of South America. They have been recorded in the Acre fossil fauna, with considerable taxonomic and ecological diversity. Novel findings from the Patos locality in Acre State have produced several specimens representing eleven taxa, including the first occurrences in the fossil record of the genera Agamyxis, Glanidium, and Trachycorystes. These taxa comprise two orders, Characiformes and Siluriformes, with four and seven taxa respectively. The taxa found in the Patos locality are representative of typical modern Amazonian assemblages found in the drainages of the region, thus suggesting substantial ecological conservatism. An updated list of the Rio Acre fossil fish fauna is consistent with previous findings in the literature regarding clustering structure in fossil assemblages during the Neogene of South America.

paleontology↗

bioRxiv2026

Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)

Obtaining large and well-resolved phylogenetic trees for neotropical clades is challenging, as many species inhabit remote regions, and sampling often relies on herbarium specimens with highly degraded DNA. Target capture provides an effective solution for retrieving molecular data from fragmentary material. However, data processing using tools generally designed for diploid organisms and single-copy loci is also challenging, particularly when events such as genome duplication and hybridisation have shaped the lineage evolution. We used dual-hybridisation to integrate Ochnaceae-specific and universal probes to reconstruct the phylogenetic relationships of Sauvagesieae, a pantropical clade with ca. 90 species mainly distributed in the northern Andes, the Brazilian Espinhaco Range, and the Amazon-Guyana region. We tested different filtering strategies involving missing data and paralogs to assess probable sources of tree discordance and topological uncertainty. We found no significant benefit in reducing tree discordance after removing entire genes due to the presence of paralogs or a high amount of missing data. Removing fragmentary sequences instead improved alignments and increased branch support of gene trees. By quantifying the proportion of SNPs, analysing the distribution of the allele frequencies, and gene-tree quartet frequencies, we found evidence of polyploidisation and hybridisation, which could reduce resolution at internal nodes, particularly in mountain clades. Our results underscore the importance of exploring the complexities of target-capture data, not only to improve phylogenetic resolution but also to understand the sources of phylogenetic conflict and the underlying molecular evolutionary processes.

genomics↗

bioRxiv2025

A flexible Bayesian method for estimating stratigraphic intervals and their co-occurrence in time

The fossil record is both incomplete and subject to a number of biases with different sources (e.g., preservational, statistical), which hinders making inferences about the past of life on earth. Stratigraphic intervals allow estimate two important quantities from the fossil record of a given lineage, its origination, and extinction times. Many models are available in the literature, although specialising in implementation and therefore resulting in limitations of application. This toolset is extended herein by proposing a flexible method which allows one to estimate origination and extinction times, as well as model preservation potential in flexible ways. The present method is more general than previous alternatives, many of which constitute special cases. A method is presented to represent the stratigraphic interval as a continuous distribution by integrating over parameter uncertainty through the use of the posterior predictive distribution, which represents the stratigraphic interval as a continuous variable in time which already incorporates parameter uncertainty, rather than a bounded interval. It is possible then to combine these distributions using conflation, to build a time probabilistic model for the co-occurrence of these intervals. Empirical examples using the method for estimating the origination and extinction times of palynomorphs and the co-occurrence time for an assemblage of unknown age in the economically important Cerrejon Formation, as well as the origination time of the marine barracudas (family Sphyraenidae), are used for illustrating the potential of the method. It is implemented in the StratIntervals.jl Julia package, which allows a large set of possible prior distributions and MCMC samplers.

evolutionary biology↗

bioRxiv2024

Fossil Freshwater Fishes from the Pliocene of northern Colombia and the Palaeogeography of northern South America

1Freshwater fishes from northern Colombia are reported from the Sincelejo and Ware formations, of Pliocene age. A total of ten taxa have been identified comprising two orders, five families, and nine genera. Characters from dental morphology, fin spines, and cranial bones are provided as taxonomic tools for the study of fossil fishes. All of the taxa are members of groups currently restricted to drainages east of the Andes, suggesting that physical drainage connection was still present by the Pliocene between the Amazon-Orinoco and trans-Andean drainages such as the Magdalena-Cauca, or that these groups persisted in the trans-Andean region at least until Pliocene times. The genera Hemidoras, Serrasalmus, and Trachely-opterichthys are new records for the fossil fish fauna of South America. The genus Zungaro represents a new record for the trans-Andean region, whereas the genus Platysilurus is for the first time in Colombia. Most of these occurrences also represent the youngest occurrences in the fossil record. Literature records are reidentified as Pygocentrus from the La Venta fauna and the earily Oligocene in Peru. These assemblages suggest that the Sincelejo and Ware formations were deposited in rivers of large size that were part of a large drainage network connected to the Amazon-Orinoco despite being currently located west of the Andes. These findings suggest that the Cordillera Oriental and the Merida Andes were not dividing yet the drainage network in northern South America by the middle to late Miocene.

paleontology↗

bioRxiv2024

The taxonomic status of Farlowella colombiensis Retzer & Page 1997 with comments on species of the F. acus species group (Loricariidae: Loricariinae).

The genus Farlowella has been historically challenging, in part due to the difficulty in defining diagnostic characters which allow to clearly set apart and identify the species. Farlowella colombiensis Retzer & Page 1997 is one of such examples, whose diagnostic characters were based on caudal-fin colour pattern, body cover ventral pattern, and details of the head. We herein reassess the taxonomic status of this species against congeners of the F. acus species group (F. acus, F. martini, F. mitoupibo, F. venezuelensis, and F. vittata). We found no significant differences between F. colombiensis and F. acus in morphometric, meristic, and discrete characters, therefore rendering Farlowella colombiensis a junior synonym of Farlowella acus. We provide remarks on different species of the F. acus group in Colombia, as well as description of sexual dimorphism in the genital papilla for the first time in the subfamily. We also provide a key to the species of the F. acus species group in Colombia.

zoology↗

bioRxiv2024

What did the dove sing to Pope Gregory? Ancestral melody reconstruction in Gregorian chant using Bayesian phylogenetics.

An attractive goal in the study of Gregorian chant melodies is reconstructing unobserved melodies as they may have been transmitted along the history of chant, especially as early chant notation does not capture pitch exactly. We propose doing this computationally using Ancestral State Reconstruction (ASR) over phylogenetic trees. Bayesian phylogenetic trees have shown promise as a tool to study the evolution of chant melodies, by inferring a plausible topology of chant transmission. However, the inferred trees cannot be used as ASR inputs directly, because they are undirected, and their branch lengths conflate time and evolutionary rate. We therefore first apply Divergence Time Estimation (DTE) to separate them and represent the tree in a directed form on the time dimension. Using ASR, we then obtain reconstructions of melodies for each of the ancestral nodes, in addition to their distribution in time obtained from DTE, and thus we obtain a phylogeny of chant melody with a music-historical interpretation. We applied this method to the Christmas Vespers dataset, and compare the results against musicological knowledge and melodies reconstructed at Solesmes using methods of contemporary philology, which shows potential for reconstructing cultural transmission through time.

evolutionary biology↗

bioRxiv2024

tbea: tools for pre- and post-processing in Bayesian evolutionary analyses

Estimating phylogenies in which branch lengths are expressed in units of absolute time is crucial for testing hypotheses in evolutionary biology. However, bioinformatic tools to pre- and post-process data from Bayesian divergence time estimation analyses are often not easily interoperable, and documenting methodological choices is not a generalized practice. The R package tbea is a tool-set to integrate biological, geological and palaeontological information to optimize the specification of models, their parameters and prior distributions in divergence times estimation analyses. tbea implements statistical models to (i) better translate time information in dating sources into the specified calibration densities, (ii) improve comparisons between prior and posterior distributions for parameters of interest, (iii) carry out inference on origination times for a set of distributions, (iv) summarise different distributions into a single one, and (v) improve the reproducibility of divergence time estimation analyses allowing users to document methodological choices. We illustrate the package functionalities by carrying out two worked examples. One on the phylogenetic relationships and divergence time estimation of South American Cynodontidae, and another one on the separation time of drainages East and West of the Andes in South America. It is expected that the tools herein available will be key when estimating events in time from sets of point estimates, as well as the combination of different posterior densities from the same parameter are useful to justifying the selection of secondary calibration points, or discussing the timing of biogeographic events when multiple sources are available.

evolutionary biology↗

bioRxiv2024

Phylogenetic and biogeographic history of the Snooks (Centropomidae: Carangiformes) spanning the closure of the Isthmus of Panama

Amphiamerican New World fishes provide a unique opportunity to explore the impact of geological processes and the formation of geographic barriers on biological diversification across both spatial and temporal dimensions. We employed phylogenetic and biogeographic methods to assess the impact of the emergence of the isthmus of Panama on the evolutionary history of Snooks. Bayesian methods were used for phylogenetic inference and divergence time estimation, incorporating the fossil record of Carangidae, Centropomidae, Istiophoriformes, Latidae, and Sphyraenidae to establish a timeline using methods of stratigraphic intervals. Biogeographic models were explored to test the hypothesis that trans-Isthmian vicariant events are coeval with the Isthmus closure. Our results suggest a sister relationship between Centropomidae and Sphyraenidae with a common ancestor that originated in the Upper Cretaceous ([~]78.18 Ma). The biogeographic model DEC+j indicated within-area speciation and dispersal (founder effect) as the primary modes of speciation in the genera Centropomus, Lates, and Sphyraena. The dispersion in the family Centropomidae was estimated from the Tropical Eastern Pacific to the Tropical Western Atlantic during the emergence of the isthmus of Panama. The alignment of divergence times with ancestral species distributions suggests a possible synchrony between the current distribution in Centropomus species and the gradual processes involved in the formation of the Isthmus of Panama during the Miocene. Furthermore, recent speciation events within each basin imply an influence of post-closure environmental conditions on the evolution of this group of fishes.

zoology↗

bioRxiv2023

Morphometrics and phylogenomics of coca (Erythroxylum spp.) illuminate its reticulate evolution, with implications for taxonomy

South American coca (Erythroxylum coca and E. novogranatense) has been a key-stone crop for many Andean and Amazonian communities for at least 8,000 years. However, over the last half century, global demand for cocaine has placed this plant in the centre of armed conflict, deforestation, and explosive growth of illegal economies. While national and international agencies progress from a war on drugs policy model towards locally appropriate, data-informed strategies to tackle coca plantations, monitoring their expansion and composition remains essential. The principal means to identify coca plants is leaf morphology, yet the extent to which it is reflected in taxonomy is uncertain. Here, we analyse the consistency of the current naming system of coca and its four closest wild relatives (the coca clade), using morphometrics, phylogenomics, and population genomics. We include the name-bearing type specimens of cocas closest wild relatives E. gracilipes and E. cataractarum. Morphometrics of 342 digitized herbarium specimens show that leaf shape and size fail to reliably discriminate between species and varieties. However, the rounder and more obovate leaves of certain coca varieties could be associated with domestication syndrome of this crop. Our phylogenomic data indicate gene flow involving monophyletic clades of E. gracilipes and the E. coca clade. These results further clarify the evolution of coca and support a taxonomic framework wherein E. gracilipes is retained as a single species. Our findings have implications for the development of cost-effective genotyping methods to effectively discriminate varieties of cultural significance from high-yielding cultivars fuelling the lucrative cocaine market.

plant biology↗

bioRxiv2021

A fossil fish assemblage from the middle Miocene of the Cocinetas Basin, northern Colombia

Freshwater fossil fish faunas have been long used to infer past drainage connections, as they are bounded by physical freshwater barriers. Here we study a middle Miocene (15.0--15.5 Ma) freshwater fish fossil fauna (Makaraipao) from the Castilletes Formation in northern Colombia, nowadays west of the Andes. We record the presence of lungfishes (Lepidosiren), pacus (Mylossoma and Piaractus), armored catfishes (Callichthyidae), and red-tail catfishes (Phractocephalus). Extant members of all those groups (except the Callichthyidae, due to lack of taxonomic resolution) are found in Amazonian faunas east of the Andes and are absent from faunas west of the Andes, indicating that the riverine systems of the Guajira Peninsula were connected to Amazonia during the middle Miocene. The similarity of La Venta (west of the Andes) and Rio Acre (east of the Andes) fish faunas during the late Miocene further indicates that the northern Andean uplift was not a complete barrier at least until[~] 11 Myr ago. However, there is a continental-wide structuring of the Miocene fish faunas that is also found in the extant faunas, suggesting that other factors such as ecological conditions, in addition to the uplift of the Andes, have shaped the biogeographic evolution of South American fish faunas.

paleontology↗