Pleistocene refugia in the Chihuahuan Desert: the phylogeographic and demographic history of the gymnosperm Ephedra compacta

Abstract

Aim We investigate the influence of late Neogene orogenic activity and Pleistocene glacial‐interglacial cycles on intraspecific divergence and demographic history in the gymnosperm shrub Ephedra compacta. We test refugia hypotheses to explain geographical patterns of genetic diversity and phylogeographic structure in a warm North American desert that reaches inter‐tropical latitudes. Location Chihuahuan Desert, Mexican Plateau, Sierra Madre Oriental, Tehuacán Valley. Methods Geographical patterns of genetic diversity were estimated using chloroplast DNA sequences of 191 individuals from 24 populations. AMOVA and SAMOVA analyses were used to assess population and phylogeographic structure, respectively. Approximate Bayesian computation (ABC) was implemented to test phylogeograhic scenarios of population divergence and demographic expansion. Ecological niche modelling (ENM) was performed to predict the potential distribution of E. compacta during the late Pleistocene and to estimate historical habitat stability. Refugia hypotheses were tested by estimating the linear associations between habitat stability, latitude and parameters of genetic diversity. Results High levels of population and phylogeographic structure were observed with six geographical groups explaining most of the variation. The best‐supported phylogeographic scenario assumed population divergence and demographic expansion during the Pleistocene. ENM predictions showed historical changes in the potential distribution of E. compacta, with a broader geographical extent in the present. Habitat stability was positively associated with population genetic diversity. Main conclusions The intraspecific population divergence and demographic expansion in E. compacta is probably associated with the glacial‐interglacial cycles of the Pleistocene. Our ENM predictions also support a scenario of habitat contraction and expansion during this time period. The phylogeographic history of E. compacta is predicted by climate refugia dynamics in which specific areas, primarily in the Mexican Plateau harbour the highest levels of habitat stability and genetic diversity.

Assembly and origin of the flora of the Chihuahuan Desert: The case of sclerophyllous Rosaceae

“…According to vegetation records, pinyon‐juniper‐oak forest was the predominant vegetation of the Chihuahuan Desert at that time (van Devender, ; van Devender & Spaulding, ; Rebernig et al, ). This expansion around the time of the Last Glacial Maximum has been detected in other ENM studies on a number of plant groups in the Chihuahuan Desert (Angulo, Amarilla, Anton, & Sosa, ; Loera et al, ; Ruiz‐Sanchez et al, ; Scheinvar et al, ). Moreover, during the Pleistocene, cooler wetter climates were mostly present the Chihuahuan Desert, and mesic woodland essentially dominated the landscape (Holmgren, Penalba, Rylander, & Betancourt, ; MacKay & Elias, ).…”

“…Furthermore, instead of considering the Mexican Plateau as a centre of origin of the flora of the Chihuahuan Desert, phylogeographic research has hypothesized that the southern region of the Mexican Plateau acted as refugium for different plant lineages that migrated either from North or South America (Loera, Ickert‐Bond, & Sosa, ; Ruiz‐Sanchez, Rodriguez‐Gomez, & Sosa, ; Scheinvar, Gámez, Castellanos‐Morales, Aguirre‐Planter, & Eguiarte, ; Vásquez‐Cruz & Sosa, ).…”

“…Likewise climate change during the last glaciation in the Chihuahuan Desert has been documented, suggesting that wet conditions in the Pleistocene were attributed to winter rainfall in contrast with the current summer rainfall regime (Metcalfe, Say, Black, & McCulloch, ). The recorded effect of these climate changes in several plant groups suggests that the glacial‐interglacial cycles of the Pleistocene caused suitable habitat contraction and expansion probably affecting distribution range (Loera et al, ; Ruiz‐Sanchez et al, ; Scheinvar et al, ).…”

Genetic Differentiation and Fragmentation in Response to Climate Change of the Narrow Endemic Psittacanthus auriculatus

“…Overall, results of current ENM and palaeomodeling show that the area currently occupied by studied species is substantially larger than it was during the LIG period and the LGM, suggesting that it has been gradually expanding northward since the LIG period. Previous phylogeographic studies that included plant populations of the Valles Centrales and the Tehuaca´n-Cuicatla´n Valley have shown that their ranges contracted during interglacials and then expanded to colonize northern xeric regions during the glacial periods (the Meztitla´n Valley and the Chihuahuan Desert; e.g., Loera, Ickert-Bond, & Sosa, 2017;Ruiz-Sanchez et al, 2012;Scheinvar et al, 2017) or expanded during the warm/humid LIG period and contracted to one or more southerly refugia during cold/dry glacial maxima (Cornejo-Romero et al, 2017).…”

A look into the past, present and future potential distributions of Talinopsis frutescens, a North American endemic lineage closely related to Cactaceae

“…There is evidence that arid environments have experienced drastic climate changes during the last glacial period (Metcalfe, 2006), especially during the Last Inter Glacial (LIG; 1.2×10 5 -1.4×10 5 years ago) and the Last Glacial Maximum (LGM; about 2.2×10 4 years ago) periods. Some studies show that several native species from arid environments have had changes in their distribution range in response to past climatic fluctuations, as is the case of Berberis trifoliolata (Berberidaceae; Angulo et al, 2017), Ephedra compacta (Ephedraceae; Loera et al, 2017), Larrea tridentata (Zygophyllaceae; Hunter et al, 2001) and Lindleya mespiloides (Rosaceae; Vásquez-Cruz and Sosa, 2016). Because T. frutescens is mainly distributed in arid environments, it is likely that those climatic oscillations affected its distribution range.…”