DOI: 10.5061/dryad.j0zpc86sv
title: Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes

description: The partitioning of ecological niches is a fundamental component of
 species diversification in adaptive radiations. However, it is presently
 unknown if and how such bursts of organismal diversity are influenced by
 temporal niche partitioning, wherein species avoid competition by being
 active during different time windows. Here, we address this question
 through profiling temporal activity patterns in the exceptionally diverse
 fauna of cichlid fishes from African Lake Tanganyika. By integrating
 week-long longitudinal behavioural recordings of over 500 individuals from
 60 species with eco-morphological and genomic information, we provide two
 lines of evidence that temporal niche partitioning facilitated this
 massive adaptive radiation. First, Tanganyikan cichlids exhibit all known
 circadian temporal activity patterns (diurnal, nocturnal, crepuscular, and
 cathemeral) and display substantial inter-specific variation in daily
 amounts of locomotion. Second, many species with similar habitat and diet
 niches occupy distinct temporal niches. Moreover, our results suggest that
 shifts between diurnal and nocturnal activity patterns are facilitated by
 a crepuscular intermediate state. In addition, genome-wide association
 studies indicate that the genetics underlying activity patterns is
 complex, with different clades associated with different combinations of
 variants. The identified variants were not associated with core circadian
 clock genes but with genes implicated in synapse function. These
 observations indicate that temporal niche partitioning contributed to
 adaptive radiation in cichlids and that many genes are associated with the
 diversity and evolution of temporal activity patterns. These data
 are the 10fps speed and x,y position tracks for 6 days for individuals for
 each of the 60 species. The behavioural analysis mostly used the 30-minute
 binned data available in the supplement of the published paper.
description: # Widespread temporal niche partitioning in an adaptive radiation of
 cichlid fishes Dataset DOI:
 [10.5061/dryad.j0zpc86sv](10.5061/dryad.j0zpc86sv) ## Description of the
 data and file structure These speed and position data were collected from
 individual fishes of different Lake Tanganyika cichlid species. In short
 data covers 6 days of data, with a 12h:12h light:dark cycle. Except for
 the dark:dark experiments (prefix: *dark-dark*), which had a 14h:10h
 light:dark cycle for the first 3 days, then 3 days of constant darkness.
 Data was acquired at 10fps. Data has been smoothed and outliers removed.
 ### Files and variables For each species, there are two file types:
 als.csv and meta.csv There is one als.csv and one meta.csv file for each
 individual animal. The als.csv data contains the tracks. The file name
 (FishID) is made in the following format: ``` FISH{date
 collected}_c{camera number}_r{row number}_{species name - not always the
 same as in Ronco et al., use Supplemental Data 1}_s{sex - not updated,
 please ignore and use sex in meta file}. ``` Columns als.csv: 1. tv_ns:
 time stamp 2. speed_mm: smoothed speed of fish, mm/second 3. x_nt: x
 position, outliers removed 4. y_nt: y position, outliers removed Columns
 meta.csv: 1. ID (FishID - see above) 2. species: species name - not always
 the same as in Ronco et al., use Supplemental Data 1 3. sex: m -male, f
 -female, u-undetermined 4. fish_length_mm: standard length of fish in mm
 5. mm_per_pixel: mm per pixel Note that species Julmrk combines data from
 Julidochromis regani and Julidochromis marksmithi, which have now been
 merged. Note that these files can be uploaded into python by the script:
 'run_combine_als' which will also adjust the timestamps of the
 very first recordings (any recording older than 20201127) which were on a
 30min shifted daily time schedule (lights on at 7.30 am instead of 7 am
 which was used for all subsequent behavioural data except the dark dark
 experiments which were on a 14h:10h light dark schedule starting at 8 am
 lights on). This script will also add Ts: time stamp, arbitrarily set to
 1970-01-02 date. Format=YYYY-MM-DD HH:MM:SS. ## Code/software Data is in
 CSV format, so it can be easily read by many software types. Scripts for
 analysis used in the manuscript can be found
 here: [https://github.com/annnic/cichlid-analysis](https://github.com/annnic/cichlid-analysis)