Journal
<p>Atyid shrimps, a key component of tropical freshwater ecosystems, face multiple anthropogenic threats and thus</p>
<p>need special attention. With more than 300 described species, the genus Caridina is the most speciose of all the</p>
<p>Caridea infra-order. Caridina spp. occupy diverse habitats in tropical freshwaters of the Indo-West Pacific region.</p>
<p>Several species complexes have been recognized, based on common morphological features, but little is known</p>
<p>about how well these morphological characteristics align with phylogenetic characteristics. Furthermore, no</p>
<p>phylogeny of the genus Caridina published so far has provided well-resolved and supported relationships among</p>
<p>different species, thus impeding the possibility of proposing evolutionary hypotheses. In this study we used next</p>
<p>generation sequencing (NGS) to provide new insights into the phylogenetic relationships among the genus</p>
<p>Caridina, focusing on two complexes: ‘Caridina nilotica’ and ‘Caridina weberi’. We collected 92 specimens belonging</p>
<p>to these two groups from most of their known geographical range, representing 50 species, for which we</p>
<p>sequenced seven mitochondrial genes and two nuclear markers using ion torrent NGS. We performed a phylogenetic</p>
<p>analysis, which yielded the first well-supported tree for the genus Caridina. On this tree were mapped the</p>
<p>geographic ranges and the habitats used by the different species, and a time calibration was tested. We found the</p>
<p>driving factors that most likely account for separation of clades are differences in habitat and to a lesser extent</p>
<p>geography. This work provides new insights into the taxonomy of this group and identifies opportunities for</p>
<p>further studies in order to fill knowledge gaps that currently impede the management and conservation of atyid</p>
<p>species.</p>
<p>1. Introduction</p>
