Biology subjects

Roch, S.

Publications and source records attributed to Roch, S..

9 recordsLinked to original sources

bioRxiv2026

Revisiting the genetics of Lake Constance Coregonids using lake-wide whole genome sequencing

Anthropogenic pressures can have detrimental impacts on fish populations, with their effective management and conservation requiring accurate monitoring tools. Yet, this is not straightforward for closely-related, co-existing species that are difficult to distinguish using simple phenotypic or genetic approaches. Coregonids are of cultural and economic importance across Europe but have faced a multitude of pressures over the last century. Yet genomic management tools are lacking. In Lake Constance, a large pre-alpine lake, stocks have drastically collapsed due to a multitude of pressures, leading to a fishery closure. Here, we adopt a cost-effective, whole genome sequencing approach for lake-wide assessment of stock composition, spatial distribution and genetic diversity of highly admixed Lake Constance whitefish (Coregonus spp.). By sequencing 983 adult and larval genomes, we show that nearly 90% of the stock is made up by one of three species, the Gangfisch (C. macrophthalmus), and define the genetic relationship between Upper and Lower Lake Constance whitefish stocks. We also identified strong mixing between Gangfisch and Blaufelchen (C. wartmanni) on traditionally specific-specific spawning grounds, and detected strong admixture in larvae, with potentially drastic impacts on the effectiveness of hatchery supplementation and stocking. Despite the collapse and admixture, species still exhibit low to moderate levels of genetic diversity, maintain ecologically-relevant genetic differences, and seem to show differences in habitat use. Overall, we present a cost-effective, translatable tool for stock-wide sequencing and genetically-informed fisheries management, with our results calling for the re-evaluation of current management practices to avoid the potential genetic mixing between species.

ecology↗

bioRxiv2025

Lower Bounds on the Sample Complexity of Species Tree Estimation when Substitution Rates Vary Across Loci

In this paper we analyze the effect of substitution rate heterogenity on the sample complexity of species tree estimation. We consider a model based on the multi-species coalescent (MSC), with the addition that gene trees exhibit random i.i.d. rates of substitution. Our first result is a lower bound on the number of loci needed to distinguish 2-leaf trees (i.e., pairwise distances) with high probability, when substitution rates satisfy a growth condition. In particular, we show that to distinguish two distances differing by length f with high probability, one requires O(f-2) loci, a significantly higher bound than the constant rate case. The second main result is a lower bound on the amount of data needed to reconstruct a 3-leaf species tree with high probability, when mutation rates are gamma distributed. In this case as well, we show that the number of gene trees must grow as O(f-2).

evolutionary biology↗

bioRxiv2024

Maximum Likelihood Estimation for Unrooted 3-Leaf Trees: An Analytic Solution for the CFN Model

AO_SCPLOWBSTRACTC_SCPLOWMaximum likelihood estimation is among the most widely-used methods for inferring phylogenetic trees from sequence data. This paper solves the problem of computing solutions to the maximum likelihood problem for 3-leaf trees under the 2-state symmetric mutation model (CFN model). Our main result is a closed-form solution to the maximum likelihood problem for unrooted 3-leaf trees, given generic data; this result characterizes all of the ways that a maximum likelihood estimate can fail to exist for generic data and provides theoretical validation for predictions made in [28]. Our proof makes use of both classical tools for studying group-based phylogenetic models such as Hadamard conjugation and reparameterization in terms of Fourier coordinates, as well as more recent results concerning the semi-algebraic constraints of the CFN model. To be able to put these into practice, we also give a complete characterization to test genericity.

evolutionary biology↗

bioRxiv2023

Phenotypic plasticity and genetic differentiation drive troglomorphic character development in European cave loach

Using a cross-fostering experiment, we provide evidence for the contribution of both genetic differentiation and phenotypic plasticity to troglomorphic character development in the recently discovered cave form of Barbatula barbatula, an evolutionarily young lineage and first cavefish described in Europe, the northernmost record. We established reproducing populations of cave- and surface-dwelling loaches to produce cave, surface, and hybrid offspring and reared the F1 fish in a common garden setting in total darkness (DD) to simulate cave conditions as well as under the natural photoperiod (DL). We observed significant differences in the occurrence and extent of typical troglomorphic target characters among the offspring groups. Regardless of rearing conditions, cave fish exhibited smaller eyes, lighter body coloration, longer barbels, and larger olfactory epithelium than seen in surface fish. Hybrids in both rearing conditions generally showed an intermediate level of these traits. Surface and hybrid DD fish differed from the DL groups, resembling the cave fish phenotype in several traits, including eye size and body pigmentation. In contrast, cave and hybrid DL fish groups resembled surface fish phenotypes. Results confirmed that troglomorphic traits arise from heritable genetic differentiation of cave from surface forms and that phenotypic plasticity contributes to the process of adaptation to novel light conditions.

evolutionary biology↗

bioRxiv2022

Statistically Consistent Rooting of Species Trees under the Multi-Species Coalescent Model

Rooted species trees are used in several downstream applications of phylogenetics. Most species tree estimation methods produce unrooted trees and additional methods are then used to root these unrooted trees. Recently, Quintet Rooting (QR) (Tabatabaee et al., ISMB and Bioinformatics 2022), a polynomial-time method for rooting an unrooted species tree given unrooted gene trees under the multispecies coalescent, was introduced. QR, which is based on a proof of identifiability of rooted 5-taxon trees in the presence of incomplete lineage sorting, was shown to have good accuracy, improving over other methods for rooting species trees when incomplete lineage sorting was the only cause of gene tree discordance, except when gene tree estimation error was very high. However, the statistical consistency of QR was left as an open question. Here, we present QR-STAR, a polynomial-time variant of QR that has an additional step for determining the rooted shape of each quintet tree. We prove that QR-STAR is statistically consistent under the multispecies coalescent model. Our simulation study under a variety of model conditions shows that QR-STAR matches or improves on the accuracy of QR. QR-STAR is available in open source form at https://github.com/ytabatabaee/Quintet-Rooting.

bioinformatics↗

bioRxiv2022

Rapid intralacustrine evolution of an invasive pelagic three-spined stickleback (Gasterosteus aculeatus) ecotype in Lake Constance.

The rapid invasion of the pelagic zone in Lake Constance by three-spined sticklebacks (Gasterosteus aculeatus) since 2012 and their subsequent drastic population growth has had stark ecosystem-wide effects, such as food-web shifts and declines in native biodiversity, including commercially important fish species. Yet, the origin of this invasive pelagic ecotype remains unclear. This study aims to determine if the pelagic ecotype arose in situ from the existing littoral population or following external colonisation, identify potential phenotypic differences between individuals from different habitats, and assess genomic signals of selection. Integrating RAD-sequencing of Lake Constance individuals and whole-genome sequence data for European outgroup populations, this study shows that the pelagic Lake Constance population likely arose recently within the lake from the littoral population, with only weak genome-wide differentiation between individuals from different habitats. This is further supported by minimal differences in meristic and morphometric traits, with shape differences only found between pelagic/inflow sticklebacks and littoral sticklebacks. Using genome scans, we identified multiple outlier loci between littoral and pelagic ecotypes across the genome, potentially suggesting early signs of sympatric speciation despite high connectivity. Furthermore, increased differentiation between pelagic and littoral sticklebacks for body shape-associated loci and the overlap of outlier loci with quantitative trait loci for ecologically relevant traits points toward a driving role of selection in this pelagic invasion. This study provides an important example of rapid ecological diversification from standing genetic variation and a rare case of littoral-pelagic ecotype divergence under high gene flow in a large oligotrophic lake. Ultimately, the results of this study will have major implications for the management of the invasive pelagic ecotype, and the entire stickleback population as a whole.

evolutionary biology↗

bioRxiv2021

On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation

We consider species tree estimation from multiple loci subject to intralocus recombination. We focus on R*, a summary coalescent-based methods using rooted triplets. We demonstrate analytically that intralocus recombination gives rise to an inconsistency zone, in which correct inference is not assured even in the limit of infinite amount of data. In addition, we validate and characterize this inconsistency zone through a simulation study that suggests that differential rates of recombination between closely related taxa can amplify the effect of incomplete lineage sorting and contribute to inconsistency.

evolutionary biology↗

bioRxiv2019

Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss

Phylogenomics--the estimation of species trees from multilocus datasets--is a common step in many biological studies. However, this estimation is challenged by the fact that genes can evolve under processes, including incomplete lineage sorting (ILS) and gene duplication and loss (GDL), that make their trees different from the species tree. In this paper, we address the challenge of estimating the species tree under GDL. We show that species trees are identifiable under a standard stochastic model for GDL, and that the polynomial-time algorithm ASTRAL-multi, a recent development in the ASTRAL suite of methods, is statistically consistent under this GDL model. We also provide a simulation study evaluating ASTRAL-multi for species tree estimation under GDL. All scripts and datasets used in this study are available on the Illinois Data Bank: https://doi.org/10.13012/B2IDB-2626814_V1.

evolutionary biology↗

bioRxiv2017

Geometry of the sample frequency spectrum and the perils of demographic inference

The sample frequency spectrum (SFS), which describes the distribution of mutant alleles in a sample of DNA sequences, is a widely used summary statistic in population genetics. The expected SFS has a strong dependence on the historical population demography and this property is exploited by popular statistical methods to infer complex demographic histories from DNA sequence data. Most, if not all, of these inference methods exhibit pathological behavior, however. Specifically, they often display runaway behavior in optimization, where the inferred population sizes and epoch durations can degenerate to 0 or diverge to infinity, and show undesirable sensitivity of the inferred demography to perturbations in the data. The goal of this paper is to provide theoretical insights into why such problems arise. To this end, we characterize the geometry of the expected SFS for piecewise-constant demographic histories and use our results to show that the aforementioned pathological behavior of popular inference methods is intrinsic to the geometry of the expected SFS. We provide explicit descriptions and visualizations for a toy model with sample size 4, and generalize our intuition to arbitrary sample sizes n using tools from convex and algebraic geometry. We also develop a universal characterization result which shows that the expected SFS of a sample of size n under an arbitrary population history can be recapitulated by a piecewise-constant demography with only{kappa} n epochs, where{kappa} n is between n/2 and 2n - 1. The set of expected SFS for piecewise-constant demographies with fewer than{kappa} n epochs is open and non-convex, which causes the above phenomena for inference from data.

evolutionary biology↗