Population genomic structure in Goodman’s mouse lemur reveals long-standing separation of Madagascar’s Central Highlands and eastern rainforests

Abstract

20The Central Highland Plateau of Madagascar is largely composed of savannah, interspersed 21 with patches of closed-canopy forests. The origins of this landscape are now accepted as long 22 preceding the arrival of humans in Madagascar, but whether savannah vegetation has remained 23 static or expanded over time remains a topic of debate. By analyzing multiple populations of 24 Goodman's mouse lemur (Microcebus lehilahytsara), a small-bodied nocturnal primate, we 25 reconstruct its phylogeographic and demographic history to serve as a proximal estimate of the 26 time at which the Central Highland and eastern forests became discontinuous. We applied 27 coalescent methods to RADseq data to infer phylogeographic relationships, population 28 structure, and migration corridors among sampling sites. Analyses revealed that forest 29 fragmentation occurred rapidly and affected both the Central Highlands and eastern forests 30 during a period of decreased precipitation near the last glacial maximum. There was clear 31 structure between Central Highland populations versus those of the eastern rainforests, but 32 there has also been historical migration across this presumed gene flow barrier. Findings 33 support origins of the Central Highland savannah that predate human arrival and demonstrate 34 that this natural landscape has long impacted the population dynamics of Goodman's mouse 35 lemur. 37Madagascar is considered to be a biodiversity hotspot with high levels of species diversity and 38 endemism [1]. Much of this diversity is at risk due to deforestation and forest fragmentation [2-39 4], which is due at least in part to human activity and agricultural practices [5,6]. But the timing 40 of and degree to which humans have transformed these closely-canopy forests and have 41 affected their connectivity has been a point of contention. Much of central Madagascar is 42 covered with savannah, which was originally thought to be the product of fires from slash-and-43 burn agriculture and cattle farming [7,8]. The best available archeological evidence places 44 humans in Madagascar between 2 thousand years ago (KYA) and 10 KYA [9-11]. This timeline 45 does coincide with an increased frequency of fire based on charcoal records from sediment 46 cores during the late to mid Holocene [12-14]. Pollen abundances from these same sediment 47 cores imply the Central Highland vegetation transitioned from woody taxa to grasses at this time 48 as well, although the transition likely began following Pleistocene glaciations [13,15] and similar 49 shifts in plant composition were not limited to the Central Highlands [16,17].50 51 Juxtaposed to the hypothesis of rapid human-mediated deforestation, ecological and 52 phylogenetic studies of Madagascar's grasses suggest the Central Highland Savannah (CHS) 53 originated well before the Holocene. Levels of endemism observed in the CHS are comparable 54 to the putatively natural grasslands of Africa [18,19]. Although few C4 lineages such as Aristida 55 and Loudetia dominate the CHS [20-22], diver...

Malagasy Polka Dot Moths (Noctuoidea: Erebidae: Arctiinae: Syntomini) of Ambohitantely—endemism in the most important relict of Central Plateau rainforest in Madagascar

“…Recent studies, not only botanical, but also those on distribution of mouse lemur species, support the latter one. This assumes that landscape composed of patches of forest and grassland had existed in the High Plateau long before human arrival, in cycles of isolation and reconnection of forest fragments driven by climate, and with a rapid fragmentation and separation from the eastern rainforests near the last glacial maximum ( Yoder et al, 2016 and papers cited therein; Joseph & Seymour, 2020 ; Tiley et al, 2020 ). In that light, referring to the forest fragments of Ambohitantely as “relict” is not quite correct if it presumes Ambohitantely was part of an extensive and continuous former dense tropical forest ( Klein, 2004 ).…”

The Diversity of Primates: From Biomedicine to Conservation Genomics

“…Methylation-based enrichment has recently been used to analyze genome-wide ancestry and introgression in Kinda and chacma baboons across a hybridation zone (136). Restriction siteassociated DNA sequencing (RAD-seq) has been used to reduce genomic complexity for SNP generation in multiple species of primates (136,143,144) to study phylogeography, speciation, and hybridization. Finally, fluorescence-activated cell sorting has recently been used to isolate primate epithelial cells directly from the fecal samples to study population structure and local adaptation in capuchin monkeys (119).…”