DOI: 10.5061/dryad.95x69p8rp
title: Testing alternative hypotheses for the decline of cichlid fish in Lake Victoria using fish fossils time series from sediment cores

description: Lake Victoria is well known for its high diversity of endemic fish species
 that provide livelihoods for millions of people. The lake garnered
 widespread attention during the twentieth century as major environmental
 and ecological changes modified the fish community with the extinction of
 ~40% of endemic cichlid species by the 1980s. Suggested causal factors
 include anthropogenic eutrophication, fishing, and introduced non-native
 species but their relative importance remains unresolved because
 monitoring data started in the 1970s when changes were already underway.
 Here, for the first time, we reconstruct two time series, covering the
 last ~200 years, of fish assemblage using fish teeth preserved in lake
 sediments. Two sediment cores Lake Victoria (Mwanza Gulf), were subsampled
 continuously at intra-decadal resolution, and teeth were identified to
 major taxa: Cyprinoidea, Haplochromini, Mochokidae, and Oreochromini. None
 of the fossils could be confidently assigned to non-native Nile Perch. Our
 data show significant decreases in haplochromine and oreochromine cichlid
 fish abundances began long before Nile Perch's arrival, while
 cyprinoids have generally been increasing. Our study is the first to
 reconstruct a time series of fish assemblage in Lake Victoria extending
 deeper back in time than the past 50 years, helping shed light on
 processes underlying Lake Victoria's biodiversity loss.
description: Two sediment cores (SC9 and SC14) were collected in 2018 from the
 Mwanza Gulf of Lake Victoria, Tanzania. The cores were taken from 12.5 m
 and 14.5 m water depths and were subsampled contiguously at 1-cm intervals
 and macrofossil analysis. Once the fossils were recovered, we calculated
 the fossil concentration (number of fossils divided by sediment volume).
 To identify temporal change points in the estimates of fossil teeth
 concentration (teeth cm<sup>3</sup>), we used the segmented
 package v1.6-4 in R (Regression Models with Break-Points and Change-Points
 Estimation) (Muggeo, 2008) and Spearman’s correlation to analyze the
 trends. 
description: # Testing alternative hypotheses for the decline of cichlid fish in Lake
 Victoria using fish fossils time series from sediment cores
 [https://doi.org/10.5061/dryad.95x69p8rp](https://doi.org/10.5061/dryad.95x69p8rp) ## Description of the data and file structure ### Datasets included: * **Sedimentcores_file_complete** = fossil dataset from sediment cores per cm depth assigned to multiple fish taxa * multiple columns: depth of sediment (cm), the year corresponding to the depth, the cored site, the category of the fossils (either bone or tooth), notes, and the lineage for teeth. * **sc9_acc_rates** and **sc14_acc_rates** = sediment accumulation rates from the two sites used to determine the fossil influx (concentration fossils multiplied by accumulation rates) * depth (cm) * volume units are per cubic cm (cm^3) * acc_rates are cm per year (cm/yr) ## Code/Software Our code can be found in Related Works Rstudio version 4.3.1 with packages: cowplot v 1.1.1, ggh4x 0.2.5, ggplot2 v3.4.2, tidyverse v2.0.0, scales v1.2.1, ggtext v0.1.2 and dplyr v1.1.2., segmented package v1.6-4, ggpubr v0.6.0