Biology subjects

Bogaard, A.

Publications and source records attributed to Bogaard, A..

4 recordsLinked to original sources

bioRxiv2024

Developmental plasticity and genetic selection shaped cereal evolution in the Early Holocene southern Levant

The domestication of plants in southwest Asia was an evolutionary process that took place over several millennia in the Early Holocene. During this time domestic species developed distinct traits that distinguish them from their wild counterparts. Current models of plant domestication emphasise the role of genetic selection in the evolution of these traits, viewing these as heritable adaptations that arose in response to selective pressures associated with human cultivation. In cereals, domestication resulted in the evolution of non-shattering rachis and increased grain size, two traits that can be tracked directly in the archaeobotanical record. Measurements of cereal grains from Early Neolithic sites indicate that grain size increase occurred prior to the evolution of non-shattering rachis, and it has been proposed that this reflects selection for larger grains under tillage, signifying pre-domestication cultivation. Here we combine morphological and metrical analysis of cereal remains, stable carbon isotope analysis, and weed ecology to test this hypothesis, using three assemblages from the southern Levant: Pre-Pottery Neolithic A Sharara (c. 9250-9200 cal BCE), Pre-Pottery Neolithic A el-Hemmeh (c. 9400-8700 cal BCE) and Late Pre-Pottery Neolithic B el-Hemmeh (c. 7500-7000 cal BCE). Our findings indicate that increased grain size in the Early Holocene is better understood as a plastic response to variation in growing conditions (specifically moisture), rather than a result of genetic selection for increased grain size under cultivation (i.e., tillage). We argue that cereal evolution in southwest Asia was initially driven by developmental plasticity, followed by genetic selection. Significance StatementCereals were amongst the earliest crops domesticated in southwest Asia and remain central to modern agriculture. We can track cereal domestication archaeologically using a suite of morphological traits, which distinguish domestic species from their wild counterparts. The process by which these traits evolved is still not fully understood but has widely been framed as genetic adaptation to cultivation. Here we seek to disentangle how two key domestication traits relating to seed dispersal and size evolved. By taking a multi-stranded approach to new archaeobotanical evidence, we demonstrate that in the Early Holocene southern Levant, cereal domestication occurred in a sequence where developmental plasticity preceded genetic selection.

plant biology↗

bioRxiv2022

Validation of manifold-based direct control for a brain-to-body neural bypass

Brain-body interfaces (BBIs) are neuroprostheses that can restore the connection between brain activity and body movements. They have emerged as a radical solution for restoring voluntary hand control in people with upper-limb paralysis. The BBI module decoding motor commands to actuate the limb from brain signals should provide the user with intuitive, accurate, and stable control. Here, we present the design and demonstration in a monkey of a novel brain decoding strategy based on the direct coupling between the activity of intrinsic neural ensembles and output variables, meant to achieve ease of learning and long-term robustness. We identified once an intrinsic low-dimensional space (called manifold) capturing the co-variation patterns of the monkeys neural activity associated to reach-to-grasp movements. We then tested the animals ability to directly control a computer cursor using cortical activation along the manifold axes and demonstrated rapid learning and stable high performance over 16 weeks of experiments. Finally, we showed that this brain decoding strategy can be effectively coupled to peripheral nerve stimulation to trigger hand movements. These results provide evidence that manifold-based direct control has promising characteristics for clinical applications of BBIs.

bioengineering↗

bioRxiv2021

Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat

Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite of its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. We report the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. We show that the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group-, and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. We discuss the origin and domestication history of the GGAtAt lineages in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool. We provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.

evolutionary biology↗

bioRxiv2020

Motor cortical dynamics are shaped by multiple distinct subspaces during naturalistic behavior

Behavior relies on continuous influx of sensory information about the body. In primates, motor cortex must integrate somatic feedback to accurately reach and manipulate objects. Yet, prior work demonstrates that motor cortex is well-described with deterministic, rather than input-driven, dynamics. Deterministic dynamics facilitate robust movement generation, but flexible motor output requires rapid responses to unexpected inputs. Here, we resolved this paradox by simultaneously recording neural population activity in motor and somatosensory cortex from four monkeys performing a naturalistic object interaction behavior resulting in occasional errors. Motor cortex was strikingly input-driven surrounding behavioral error correction. Intriguingly, input-driven dynamics were isolated to a subspace of the population activity that putatively captured somatosensory feedback. Using electrical stimulation of ascending somatosensory tracts, we causally verified that this feedback subspace captured peripheral inputs to cortex. Our results demonstrate that cortical activity is compartmentalized within distinct subspaces, enabling flexible integration of salient inputs for robust behavior.

neuroscience↗