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.

Dataset DOI: 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:

tv_ns: time stamp
speed_mm: smoothed speed of fish, mm/second
x_nt: x position, outliers removed
y_nt: y position, outliers removed

Columns meta.csv:

ID (FishID - see above)
species: species name - not always the same as in Ronco et al., use Supplemental Data 1
sex: m -male, f -female, u-undetermined
fish_length_mm: standard length of fish in mm
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

Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes

Data files

Abstract

Description of the data and file structure

Files and variables

Code/software

Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes

Data files

Abstract

README: Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes

Description of the data and file structure

Files and variables

Code/software

Works referencing this dataset