PT  - JOURNAL ARTICLE
AU  - Frederik Van den Broeck
AU  - Nicholas J. Savill
AU  - Hideo Imamura
AU  - Mandy Sanders
AU  - Ilse Maes
AU  - Sinclair Cooper
AU  - David Mateus
AU  - Marlene Jara
AU  - Vanessa Adaui
AU  - Jorge Arevalo
AU  - Alejandro Llanos-Cuentas
AU  - Lineth Garcia
AU  - Elisa Cupolillo
AU  - Michael Miles
AU  - Matthew Berriman
AU  - Achim Schnaufer
AU  - James A. Cotton
AU  - Jean-Claude Dujardin
TI  - Ecological divergence and hybridization of Neotropical <em>Leishmania</em> parasites
AID  - 10.1101/824912
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 824912
4099  - http://biorxiv.org/content/early/2019/11/22/824912.short
4100  - http://biorxiv.org/content/early/2019/11/22/824912.full
AB  - The tropical Andes is an important natural laboratory to understand speciation and diversification in many taxa. Here, we examined the evolutionary history of parasites of the Leishmania braziliensis species complex based on whole genome sequencing of 67 isolates from 47 localities in Peru. We firstly show the origin of near-clonal Andean Leishmania lineages that diverged from admixed Amazonian ancestors, accompanied by a significant reduction in genome diversity and large structural variations implicated in host-parasite interactions. Beside a clear dichotomy between Andean and Amazonian species, patterns of population structure were strongly associated with biogeographical origin. Molecular clock analyses and ecological niche modeling suggested that the history of diversification of the Andean lineages is limited to the Late Pleistocene and intimately associated with habitat contractions driven by climate change. These results support a wider model on trypanosomatid evolution where major parasite lineages emerge through ecological fitting. Second, genome-scale analyses provided evidence of meiotic recombination between Andean and Amazonian Leishmania species, resulting in full-genome hybrids. The mitochondrial genome of these hybrids consisted of homogeneous uniparental maxicircles, but minicircles originated from both parental species, leaving a mosaic ancestry of minicircle-encoded guide RNA genes. We further show that mitochondrial minicircles - but not maxicircles - show a similar evolutionary pattern as the nuclear genome, suggesting that biparental inheritance of minicircles is universal and may be important to alleviate maxicircle-nuclear incompatibilities. By comparing full nuclear and mitochondrial genome ancestries, our data expands our appreciation on the genetic consequences of diversification and hybridization in parasitic protozoa.