BackgroundBambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae.ResultsHere a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from Arundinarieae. Trees generated using full plastome sequences support the previously recovered monophyletic relationship between Bambuseae and Olyreae. In addition to these relationships, several unique plastome features are uncovered including the first mitogenome-to-plastome horizontal gene transfer observed in monocots.ConclusionsPhylogenomic agreement with previous published phylogenies reinforces the validity of these studies. Additionally, this study presents the first published plastomes from Neotropical woody bamboos and the first full plastome phylogenomic study performed within the herbaceous bamboos. Although the phylogenomic tree presented in this study is largely robust, additional studies using nuclear genes support monophyly in woody bamboos as well as hybridization among previous woody bamboo lineages. The evolutionary history of the Bambusoideae could be further clarified using transcriptomic techniques to increase sampling among nuclear orthologues and investigate the molecular genetics underlying the development of woody and floral tissues.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0321-5) contains supplementary material, which is available to authorized users.

Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests–among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage-specific, and thus difficult to capture in a simple conservation strategy.

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BackgroundEcological adaptation to host taxa is thought to result in mistletoe speciation via race formation. However, historical and ecological factors could also contribute to explain genetic structuring particularly when mistletoe host races are distributed allopatrically. Using sequence data from nuclear (ITS) and chloroplast (trnL-F) DNA, we investigate the genetic differentiation of 31 Psittacanthus schiedeanus (Loranthaceae) populations across the Mesoamerican species range. We conducted phylogenetic, population and spatial genetic analyses on 274 individuals of P. schiedeanus to gain insight of the evolutionary history of these populations. Species distribution modeling, isolation with migration and Bayesian inference methods were used to infer the evolutionary transition of mistletoe invasion, in which evolutionary scenarios were compared through posterior probabilities.ResultsOur analyses revealed shallow levels of population structure with three genetic groups present across the sample area. Nine haplotypes were identified after sequencing the trnL-F intergenic spacer. These haplotypes showed phylogeographic structure, with three groups with restricted gene flow corresponding to the distribution of individuals/populations separated by habitat (cloud forest localities from San Luis Potosí to northwestern Oaxaca and Chiapas, localities with xeric vegetation in central Oaxaca, and localities with tropical deciduous forests in Chiapas), with post-glacial population expansions and potentially corresponding to post-glacial invasion types. Similarly, 44 ITS ribotypes suggest phylogeographic structure, despite the fact that most frequent ribotypes are widespread indicating effective nuclear gene flow via pollen. Gene flow estimates, a significant genetic signal of demographic expansion, and range shifts under past climatic conditions predicted by species distribution modeling suggest post-glacial invasion of P. schiedeanus mistletoes to cloud forests. However, Approximate Bayesian Computation (ABC) analyses strongly supported a scenario of simultaneous divergence among the three groups isolated recently.ConclusionsOur results provide support for the predominant role of isolation and environmental factors in driving genetic differentiation of Mesoamerican parrot-flower mistletoes. The ABC results are consistent with a scenario of post-glacial mistletoe invasion, independent of host identity, and that habitat types recently isolated P. schiedeanus populations, accumulating slight phenotypic differences among genetic groups due to recent migration across habitats. Under this scenario, climatic fluctuations throughout the Pleistocene would have altered the distribution of suitable habitat for mistletoes throughout Mesoamerica leading to variation in population continuity and isolation. Our findings add to an understanding of the role of recent isolation and colonization in shaping cloud forest communities in the region.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0648...

Aim Cloud forests of northern Mesoamerica represent the northern and southern limit of the contact zone between species otherwise characteristic of North or South America. Several phylogeographic studies featuring temperate conifer species have improved our understanding of species responses to environmental changes. In contrast, conifer species that presumably colonized northern Mesoamerica from South America are far less studied. A phylogeographic study of Podocarpus matudae (Podocarpaceae) was conducted to identify any major evolutionary divergences or disjunctions across its range and to determine if its current distribution is associated with pre-Quaternary climatic and/or longdistance dispersal events. Location Northern Mesoamerica (Mexico and Guatemala).Methods Sixteen populations (157 individuals) of P. matudae were screened for variation at two plastid DNA markers. The intra-specific phylogenetic relationships among haplotypes were reconstructed using Bayesian inference. Population genetic analyses were undertaken to gain insight into the evolutionary history of these populations. To test whether genetic divergence among populations occurred at different time-scales plastid DNA sequence data and fossil-and coalescent-based calibrations were integrated. ResultsThe combination of plastid markers yielded 11 haplotypes. Differentiation among populations based on DNA variation (G ST ) (0.707, SE 0.0807) indicated a clear population structure in P. matudae. Differentiation for ordered alleles (N ST ) (0.811, SE 0.0732) was higher than that for G ST , indicating phylogeographical structure in P. matudae. Most of the total variation (81.3%, P < 0.0001) was explained by differences among populations. The estimated divergence time between the unique haplotypes from a Guatemalan population and the two most common haplotypes from the Sierra Madre Oriental in Mexico was between 10 and 20 Ma, and further haplotype divergence in the poorly resolved clade of the Sierra Madre Oriental occurred between 3 and 0.5 Ma.Main conclusions Divergence estimations support the hypothesis that extant Podocarpus matudae populations are pre-Quaternary relicts. This finding is consistent with fossil and pollen data that support a Miocene age for temperate floristic elements in Mesoamerican cloud forests, whereas further haplotype divergence within the Sierra Madre Oriental, Chiapas and Guatemala occurred more recently, coinciding with Pleistocene cloud forest refugia.

Aim Our aims were to determine the pattern of genetic variation in the endemic shrub Nolina parviflora, and to evaluate the influence of the geological history of the Trans‐Mexican Volcanic Belt (TMVB) and nearby mountainous regions on plant population divergence. Location Trans‐Mexican Volcanic Belt, Sierra Madre Occidental, Sierra Madre Oriental and Sierra Madre del Sur mountain ranges in Mexico. Methods Twenty‐eight populations (210 individuals) were sequenced for one nuclear (rpb2) and two chloroplast (trnL–F and psbA–trnH) DNA markers. Intraspecific phylogenetic relationships among haplotypes were reconstructed, and molecular dating, population genetic analyses and group testing were performed on the data. Isolation‐by‐distance analysis was conducted for the populations spanning the distribution of the species. Results Twenty‐four chloroplast marker haplotypes and 36 rpb2 haplotypes were recovered from the populations sampled. The combined marker phylogeny indicates the presence of two well‐supported clades within the N. parviflora populations. Clade 1 includes populations from Jalisco and Zacatecas and Clade 2 comprises the remaining populations. We found an east–west geographical pattern of chloroplast DNA (cpDNA) haplotype distribution, indicating a lack of gene flow between these two regions. Divergence time estimates indicate an Oligocene to mid‐Miocene divergence between Nolina and Dasylirion. Divergence estimates for Clade 1 are from the mid‐Miocene to early Pleistocene, and for Clade 2 from the early Miocene to mid‐Pliocene. Values of cpDNA GST (0.702) indicate a strong population structure and differentiation. A spatial analysis of molecular variance indicates 11 groups among the sampled populations and detects various well‐supported geographical barriers. Main conclusions Divergence time estimates suggest a correlation between the time of divergence between distinct N. parviflora populations and periods of uplift in the TMVB. We infer that the orogeny of this mountain range played an important role in driving the diversification of plant populations in central Mexico by creating topographical barriers that limited gene flow.

We investigate the genetic variation between populations of the American sweetgum (Liquidambar styraciflua), a tree species with a disjunct distribution between northeastern Texas and Mexico, by analyzing sequences of two chloroplast DNA plastid regions in Mesoamerica. Our results revealed phylogeographical structure, with private haplotypes distributed in unique environmental space at either side of the Trans-Mexican Volcanic Belt, and a split in the absence of gene flow dating back ca. 4.2–1.4 million years ago (MYA). Species distribution modeling results fit a model of refugia along the Gulf and Atlantic coasts but the present ranges of US and Mesoamerican populations persisted disjunct during glacial/interglacial cycles. Divergence between the US and Mesoamerican (ca. 8.4–2.8 MYA) populations of L. styraciflua and asymmetrical gene flow patterns support the hypothesis of a long-distance dispersal during the Pliocene, with fragmentation since the most recent glacial advance (120,000 years BP) according to coalescent simulations and high effective migration rates from Mesoamerica to the USA and close to zero in the opposite direction. Our findings implicate the Trans-Mexican Volcanic Belt as a porous barrier driving genetic divergence of L. styraciflua, corresponding with environmental niche differences, during the Pliocene to Quaternary volcanic arc episode 3.6 MYA, and a Mesoamerican origin of populations in the USA.

Aim A phylogeographic study of the endemic Mexican tulip poppy Hunnemannia fumariifolia (Papaveraceae) was conducted to determine: (1) the historical processes that influenced its geographical pattern of genetic variation;(2) whether isolation by distance was one of the main factors that caused genetic divergence in populations of this species; and (3) whether genetic flow still exists between populations from northern arid zones (Chihuahuan Desert and Sierra Madre Oriental) and those from southern arid zones (Tehuacán-Cuicatlán Valley) -populations that are separated by the Transvolcanic Belt. Location Xerophytic vegetation in Mexico.Methods Chloroplast DNA (cpDNA) sequences of three regions, trnH-psbA, rpl32-trnL(UAG) and ndhF-rpl32, were obtained for 85 individuals from 17 populations sampled in the field, covering the entire range of H. fumariifolia. The evolutionary history of these populations was investigated using a nested clade phylogeographic analysis and also by conducting various population genetic analyses. ResultsIn total, 17 haplotypes were detected, 14 of which were found in the Sierra Madre Oriental. Differentiation among populations based on cpDNA variation (G ST = 0.787, SE 0.0614) indicated population structure in H. fumariifolia, corroborated by a fixation index (F ST ) of 0.907. Results from analysis of molecular variance found that most of the total variation (90.71%, P < 0.001) was explained by differences among populations. Three regions were determined based on geological correspondence -the Chihuahuan Desert, Sierra Madre Oriental and Tehuacán-Cuicatlán Valley -and the variation between them was significant (43.39%, P < 0.001). Results of a Mantel test showed a significant correlation between genetic and geographic distances (r = 0.511; P = 0.0001), suggesting a pattern of isolation by distance, which was corroborated by nested clade phylogeographic analysis. Mismatch distribution analysis indicated a sudden demographic expansion.Main conclusions Our study found that isolation by distance influenced genetic divergence in populations of H. fumariifolia. The finding that allopatric fragmentation influenced genetic divergence in populations in the Sierra Madre Oriental may be a reflection of the complex geology of the area. Our results suggest that the areas located in the north of the Sierra Madre Oriental acted as post-glacial refugia for some populations.