Improved allometric models to estimate the aboveground biomass of tropical trees

Terrestrial carbon stock mapping is important for the successful implementation of climate change mitigation policies. Its accuracy depends on the availability of reliable allometric models to infer oven-dry aboveground biomass of trees from census data. The degree of uncertainty associated with previously published pantropical aboveground biomass allometries is large. We analyzed a global database of directly harvested trees at 58 sites, spanning a wide range of climatic conditions and vegetation types (4004 trees ≥ 5 cm trunk diameter). When trunk diameter, total tree height, and wood specific gravity were included in the aboveground biomass model as covariates, a single model was found to hold across tropical vegetation types, with no detectable effect of region or environmental factors. The mean percent bias and variance of this model was only slightly higher than that of locally fitted models. Wood specific gravity was an important predictor of aboveground biomass, especially when including a much broader range of vegetation types than previous studies. The generic tree diameter-height relationship depended linearly on a bioclimatic stress variable E, which compounds indices of temperature variability, precipitation variability, and drought intensity. For cases in which total tree height is unavailable for aboveground biomass estimation, a pantropical model incorporating wood density, trunk diameter, and the variable E outperformed previously published models without height. However, to minimize bias, the development of locally derived diameter-height relationships is advised whenever possible. Both new allometric models should contribute to improve the accuracy of biomass assessment protocols in tropical vegetation types, and to advancing our understanding of architectural and evolutionary constraints on woody plant development.

Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

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PREMISE OF THE STUDY

Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.•

METHODS

Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).•

KEY RESULTS

The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.•

CONCLUSIONS

The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.

High proportion of cactus species threatened with extinction

A high proportion of plant species is predicted to be threatened with extinction in the near future. However, the threat status of only a small number has been evaluated compared with key animal groups, rendering the magnitude and nature of the risks plants face unclear. Here we report the results of a global species assessment for the largest plant taxon evaluated to date under the International Union for Conservation of Nature (IUCN) Red List Categories and Criteria, the iconic Cactaceae (cacti). We show that cacti are among the most threatened taxonomic groups assessed to date, with 31% of the 1,478 evaluated species threatened, demonstrating the high anthropogenic pressures on biodiversity in arid lands. The distribution of threatened species and the predominant threatening processes and drivers are different to those described for other taxa. The most significant threat processes comprise land conversion to agriculture and aquaculture, collection as biological resources, and residential and commercial development. The dominant drivers of extinction risk are the unscrupulous collection of live plants and seeds for horticultural trade and private ornamental collections, smallholder livestock ranching and smallholder annual agriculture. Our findings demonstrate that global species assessments are readily achievable for major groups of plants with relatively moderate resources, and highlight different conservation priorities and actions to those derived from species assessments of key animal groups.

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.

DIRECT AND INDIRECT ESTIMATES OF NEIGHBORHOOD AND EFFECTIVE POPULATION SIZE IN A TROPICAL PALM, ASTROCARYUM MEXICANUM

To estimate the relative importance of genetic drift, the effective population size ∗∗∗(N_e ) can be used. Here we present estimates of the effective population size and related measures in Astrocaryum mexicanum, a tropical palm from Los Tuxtlas rain forest, Veracruz, Mexico. Seed and pollen dispersal were measured. Seeds are primarily dispersed by gravity and secondarily dispersed by small mammals. Mean primary and secondary dispersal distances for seeds were found to be small (0.78 m and 2.35 m, respectively). A. mexicanum is beetle pollinated and pollen movements were measured by different methods: a) using fluorescent dyes, b) as the minimum distance between active female and male inflorescences, and c) using rare allozyme alleles as genetic markers. All three estimates of pollen dispersal were similar, with a mean of approximately 20 m. Using the seed and pollen dispersal data, the genetic neighborhood area (A) was estimated to be 2,551 m² . To obtain the effective population size, three different overlapping generation methods were used to estimate an effective density with demographic data from six permanent plots. The effective density ranged from 0.040 to 0.351 individuals per m² . The product of effective density and neighborhood area yields a direct estimate of the neighborhood effective population size (N_b ). N_b ranged from 102 to 895 individuals. Indirect estimates of population size and migration rate (Nm) were obtained using F_st for five different allozymic loci for both adults and seeds. We obtained a range of Nm from 1.2 to 19.7 in adults and a range of Nm from 4.0 to 82.6 for seeds. We discuss possible causes of the smaller indirect estimates of Nm relative to the direct and compare our estimates with values from other plant populations. Gene dispersal distances, neighborhood size, and effective population size in A. mexicanum are relatively high, suggesting that natural selection, rather than genetic drift, may play a dominant role in patterning the genetic variation in this tropical palm.

Undervalued potential of crassulacean acid metabolism for current and future agricultural production

The potential for crassulacean acid metabolism (CAM) to support resilient crops that meet demands for food, fiber, fuel, and pharmaceutical products far exceeds current production levels. This review provides background on five families of plants that express CAM, including examples of many species within these families that have potential agricultural uses. We summarize traditional uses, current developments, management practices, environmental tolerance ranges, and economic values of CAM species with potential commercial applications. The primary benefit of CAM in agriculture is high water use efficiency that allows for reliable crop yields even in drought conditions. Agave species, for example, grow in arid conditions and have been exploited for agricultural products in North and South America for centuries. Yet, there has been very little investment in agricultural improvement for most useful Agave varieties. Other CAM species that are already traded globally include Ananas comosus (pineapple), Aloe spp., Vanilla spp., and Opuntia spp., but there are far more with agronomic uses that are less well known and not yet developed commercially. Recent advances in technology and genomic resources provide tools to understand and realize the tremendous potential for using CAM crops to produce climate-resilient agricultural commodities in the future.

Natural selection maintains species despite frequent hybridization in the desert shrub Encelia

Natural selection is an important driver of genetic and phenotypic differentiation between species. For species in which potential gene flow is high but realized gene flow is low, adaptation via natural selection may be a particularly important force maintaining species. For a recent radiation of New World desert shrubs (Encelia: Asteraceae), we use fine-scale geographic sampling and population genomics to determine patterns of gene flow across two hybrid zones formed between two independent pairs of species with parapatric distributions. After finding evidence for extremely strong selection at both hybrid zones, we use a combination of field experiments, high-resolution imaging, and physiological measurements to determine the ecological basis for selection at one of the hybrid zones. Our results identify multiple ecological mechanisms of selection (drought, salinity, herbivory, and burial) that together are sufficient to maintain species boundaries despite high rates of hybridization. Given that multiple pairs of Encelia species hybridize at ecologically divergent parapatric boundaries, such mechanisms may maintain species boundaries throughout Encelia.

Effects of plant size and weather on the flowering phenology of the organ pipe cactus (Stenocereus thurberi)

BACKGROUND AND AIMS

Flowering phenology is a critical life-history trait that influences reproductive success. It has been shown that genetic, climatic and other factors such as plant size affect the timing of flowering and its duration. The spatial and temporal variation in the reproductive phenology of the columnar cactus Stenocereus thurberi and its association with plant size and environmental cues was studied.

METHODS

Flowering was monitored during 3 years in three populations of S. thurberi along a latitudinal gradient. Plant size was related to phenological parameters. The actual and past weather were used for each site and year to investigate the environmental correlates of flowering.

KEY RESULTS

There was significant variation in the timing of flowering within and among populations. Flowering lasted 4 months in the southern population and only 2 months in the northern population. A single flowering peak was evident in each population, but ocurred at different times. Large plants produced more flowers, and bloomed earlier and for a longer period than small plants. Population synchrony increased as the mean duration of flowering per individual decreased. The onset of flowering is primarily related to the variance in winter minimum temperatures and the duration to the autumn-winter mean maximum temperature, whereas spring mean maximum temperature is best correlated with synchrony.

CONCLUSIONS

Plant size affects individual plant fecundity as well as flowering time. Thus the population structure strongly affects flowering phenology. Indications of clinal variation in the timing of flowering and reproductive effort suggest selection pressures related to the arrival of migrating pollinators, climate and resource economy in a desert environment. These pressures are likely to be relaxed in populations where individual plants can attain large sizes.

Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus

Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (Hsp = 0.207, HBT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θB = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics.

Understanding and predicting frost-induced tropical tree mortality patterns

Extreme climatic and weather events are increasing in frequency and intensity across the world causing episodes of widespread tree mortality in many forested ecosystems. However, we have a limited understanding about which local factors influence tree mortality patterns, restricting our ability to predict tree mortality, especially within topographically complex tropical landscapes with a matrix of mature and secondary forests. We investigated the effects of two major local factors, topography and forest successional type, on climate-induced tropical tree mortality patterns using an observational and modeling approach. The northernmost Neotropical dry forest endured an unprecedented episode of frost-induced tree mortality after the historic February 2011 cold wave hit northwestern Mexico. In a moderately hilly landscape covering mature and secondary tropical dry forests, we surveyed 454 sites for the presence or absence of frost-induced tree mortality. In addition, across forty-eight 1 ha plots equally split into the two forest types, we examined 6,981 woody plants to estimate a frost-disturbance severity metric using the density of frost-killed trees. Elevation is the main factor modulating frost effects regardless of forest type. Higher occurrence probabilities of frost-induced tree mortality at lowland forests can be explained by the strong influence of elevation on temperature distribution since heavier cold air masses move downhill during advective frosts. Holding elevation constant, the probability of frost-induced tree mortality in mature forests was twice that of secondary forests but severity showed the opposite pattern, suggesting a cautious use of occurrence probabilities of tree mortality to infer severity of climate-driven disturbances. Extreme frost events, in addition to altering forest successional pathways and ecosystem services, likely maintain and could ultimately shift latitudinal and altitudinal range margins of Neotropical dry forests.

Geographic variation in reproductive success of Stenocereus thurberi (Cactaceae): Effects of pollination timing and pollinator guild

PREMISE OF THE STUDY

It has been proposed that species of columnar cacti from dry tropical areas depend on bats for their reproduction, whereas species from dry subtropical areas are also pollinated by other species. To test this hypothesis, we examined the effects of pollinator guild and of variation in time and space on the reproductive success of a widespread species. •

METHODS

Changes in fruit set, seed set, and pollinator activity through time were recorded in three widely separated populations of Stenocereus thurberi. Breeding system and sources of pollination limitation were determined by controlled pollinator exclusions in each population. •

KEY RESULTS

Significant differences were found in the timing of activity and in the effectiveness of pollinators among sites. In the northern and central populations, reproductive success depends on bats, whereas in the southern population a combination of pollinators was more effective. No difference between open and hand cross-pollination treatments was found in the northern and central populations, which suggests no pollen limitation. However, significant differences were detected in the southern population, which indicates temporal differences in pollinator abundance or arrival time. •

CONCLUSIONS

Local variation in pollinator assemblages and reproductive success could greatly affect the evolution of pollination systems. The pattern of generalist pollination in the southernmost populations and specialized pollination in the central and northern populations contradicts the hypothesis of latitudinal variation. In the absence of nocturnal pollinators, the accumulated nectar can sustain visits by diurnal pollinators, a bet-hedging strategy that increases the chances of fruit set in some populations.

[Biodiversity and depressive symptoms in Mexican adults: Exploration of beneficial environmental effects]

INTRODUCTION

Depression is a highly prevalent illness among adults, and it is the second most frequently reported mental disorder in urban settings in México. Exposure to natural environments and its components may improve the mental health of the population.

OBJECTIVE

To evaluate the association between biodiversity indicators and the prevalence of depressive symptoms among the adult population (20 to 65 years of age) in México.

MATERIALS AND METHODS

Information from the Encuesta Nacional de Salud y Nutrición 2006 (ENSANUT 2006) and the Compendio de Estadísticas Ambientales 2008 was analyzed. A biodiversity index was constructed based on the species richness and ecoregions in each state. A multilevel logistic regression model was built with random intercepts and a multiple logistic regression was generated with clustering by state.

RESULTS

The factors associated with depressive symptoms were being female, self-perceived as indigenous, lower education level, not living with a partner, lack of steady paid work, having a chronic illness and drinking alcohol. The biodiversity index was found to be inversely associated with the prevalence of depressive symptoms when defined as a continuous variable, and the results from the regression were grouped by state (OR=0.71; 95% CI = 0.59-0.87).

CONCLUSIONS

Although the design was cross-sectional, this study adds to the evidence of the potential benefits to mental health from contact with nature and its components.

Nonlinear modeling of saguaro growth rates reveals the importance of temperature for size-dependent growth

PREMISE

The saguaro cactus is an iconic species of the Sonoran Desert. Its individual growth rates have been investigated for over 100 years. Its growth dynamics have been studied using phenomenological models intended to estimate growth, but not to understand the underlying biological processes. Most studies have suggested summer rainfall as the sole factor determining saguaro growth, overlooking the influence of other factors related to the process of growth.

METHODS

We analyzed the annual growth rates for 13 saguaro populations in the Sonoran Desert using nonlinear models. These are better suited to analyze growth since they consider the fact that maximum growth rates diminish just before the onset of reproduction. We related model parameters to the local climate.

RESULTS

The most parsimonious model was the Ricker function that described growth considering cactus decline with age. Variance in temperature, rather than precipitation, was more closely related to growth. Higher variance in temperature at the beginning of the warm season was detrimental to saguaro growth.

CONCLUSIONS

Simple nonlinear equations modeled growth rate using biologically interpretable parameters related to climate factors. Because the temperature is projected to increase in both mean and variance by climate change, the population dynamics of this iconic cactus are likely to be affected.

Episodic recruitment in the saguaro cactus is driven by multidecadal periodicities

Each year, an individual mature large saguaro cactus produces about one million seeds in attractive juicy fruits that lure seed predators and seed dispersers to a 3-month feast. From the million seeds produced, however, only a few will persist into mature saguaros. A century of research on saguaro population dynamics has led to the conclusion that saguaro recruitment is an episodic event that depends on the convergence of suitable conditions for survival during the critical early stages. Because most data have been collected in Arizona, particularly in the surroundings of Tucson, most research has relied on a limited amount of environmental variation. In this study, we upscaled this knowledge on saguaro recruitment to a regional scale with a new method that used the inverse-growth modeling of 1,487 saguaros belonging to 13 populations in a latitudinal gradient ranging from arid desert to tropical thornscrub forest in Sonora, Mexico. Using generalized linear and additive mixed models, we created two 110-yr-long saguaro recruitment curves: one driven only by previous size, and the second driven by size, drought, and soil structure. We found evidence that saguaro recruitment is indeed episodic, with periodicities of 20-30 yr, possibly related to strong El Niño Southern Oscillation events. Our results suggest that saguaros rely on multidecadal periodic pulses of good beneficial years to incorporate new individuals into their populations. Inverse-growth modeling can be used in a wide variety of plant species to study their recruitment dynamics.

Population decline of the saguaro cactus throughout its distribution is associated with climate change

BACKGROUND AND AIMS

Climate change is a global phenomenon affecting species, which in arid regions will translate into more frequent and intense periods of drought. The Sonoran Desert is becoming hotter and drier, and many organisms are rapidly changing in abundance and distribution. These population attributes depend directly on the dynamics of the population, which in turn depends on the vital rates of its individuals; yet few studies have documented the effects of climate change on the population dynamics of keystone species such as the saguaro cactus (Carnegiea gigantea). Although saguaros have traits that enable them to withstand present environmental conditions, climate change could make them vulnerable if forced beyond their tolerance limits.

METHODS

We evaluated the effect of climate change on 13 saguaro populations spanning most of the species' distribution range. Using field data from 2014 to 2016, we built an integral projection model (IPM) describing the environmentally explicit dynamics of the populations. We used this IPM, along with projections of two climate change scenarios and one no-change scenario, to predict population sizes (N) and growth rates (λ) from 2017 to 2099 and compared these scenarios to demonstrate the effect of climate change on the future of saguaro cactuses.

KEY RESULTS

We found that all populations will decline, mainly due to future increases in drought, mostly hindering recruitment. However, the decline will be different across populations, since those located near the coast will be affected by harsher drought events than those located further inland.

CONCLUSIONS

Our study demonstrates that climate change and its associated increase in drought pose a significant threat to the saguaro cactus populations in the Sonoran Desert. Our findings indicate that the recruitment of saguaros, vital for establishing new individuals, is particularly vulnerable to intensifying drought conditions. Importantly, regional climate trends will have different impacts on saguaro populations across their distribution range.

Difference in Germination Traits between Congeneric Native and Exotic Species May Affect Invasion

Germination traits are components of invasion potential, and comparing seed traits in sympatric native and invasive species can offer insights into the invasion process. We characterized seed germination traits and how they influenced the success of Eragrostis mexicana, a native species, and Eragrostis tenuifolia, an exotic species (Poaceae) in Mexico, in the context of their potential for biological invasion. Seeds from both species were collected from four sites in a natural protected area in Mexico City, and the germination of seeds of different ages was conducted in experiments at different temperatures. E. tenuifolia exhibited higher germination percentages than the native E. mexicana across all treatments. Seed age had differential effects, with older seeds of the native E. mexicana germinating better, while E. tenuifolia performed better with younger seeds. Temperature positively impacted germination for both species, although E. mexicana was limited at lower temperatures. Exotic E. tenuifolia can germinate over a wider temperature range with earlier germination rates, and generate a seed bank lasting several years, which may contribute to naturalization. The importance of germination traits in the context of invasive species establishment underscores the potential role of seed banks in facilitating biological invasions.

Human-made small reservoirs alter dryland hydrological connectivity

Our research shed light on the distribution, number, and impact of small reservoirs (SRs) on rural dryland water availability and hydrology. We measured the storage capacity, relationship to environmental variables, and effects on the hydrology of all SRs (1225) found within a Sonoran Desert basin. SRs were predominantly associated with Tertiary conglomerates and Quaternary alluvium and were less common in extrusive rocks. A higher concentration of reservoirs was observed in woodlands and thornscrub, with fewer SRs in desertscrub than anticipated by chance. The average size of these small reservoirs was 5205 m2. All SRs reached full storage capacity during the rainy season, but only 20 % retained water throughout the year. Furthermore, our analysis revealed a significant impact on basin connectivity, with only 41 % of superficial drainage being connected. Notably, two large dams were found to disconnect 26 % of the basin. Despite their relatively small watershed footprint, SRs were found to be responsible for disconnecting 33 % of the total basin area. The magnitude of rainfall events played a crucial role in connectivity dynamics. Low-magnitude rainfall events led to sediment retention in SRs, reducing connectivity, while moderate events increased connectivity by repeatedly filling SRs. High-magnitude events reshaped channels, transported sediments, and enhanced overall connectivity. The concentration of SRs in the upper reaches of the basin coincides with higher stocking rates. SRs, are relatively recent additions to desert landscapes, impacting ecological dynamics. Their construction and use fragment an already disjointed basin, thereby restricting water retention by larger dams. These findings emphasize the intricate relationship between SRs, rainfall occurrences, and the overall connectivity of the basin. We underline that documenting the cumulative effects of SRs yields valuable insights for managing water resources in arid ecosystems.

Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactus

Genetic differentiations and phylogeographical patterns are controlled by the interplay between spatial isolation and gene flow. To assess the extent of gene flow across an oceanic barrier, we explored the effect of the separation of the peninsula of Baja California on the evolution of mainland and peninsular populations of the long-lived columnar cactus Stenocereus thurberi. We analyzed twelve populations throughout the OPC distribution range to assess genetic diversity and structure using chloroplast DNA sequences. Genetic diversity was higher (Hd = 0.81), and genetic structure was lower (GST = 0.143) in mainland populations vs peninsular populations (Hd = 0.71, GST = 0.358 respectively). Genetic diversity was negatively associated with elevation but positively with rainfall. Two mainland and one peninsular ancestral haplotypes were reconstructed. Peninsular populations were as isolated among them as with mainland populations. Peninsular haplotypes formed a group with one mainland coastal population, and populations across the gulf shared common haplotypes giving support to regular gene flow across the Gulf. Gene flow is likely mediated by bats, the main pollinators and seed dispersers. Niche modeling suggests that during the Last Glacial Maximum (c. 130 ka), OPC populations shrank to southern locations. Currently, Stenocereus thurberi populations are expanding, and the species is under population divergence despite ongoing gene flow. Ancestral populations are located on the mainland and although vicariant peninsular populations cannot be ruled out, they are likely the result of gene flow across the seemingly formidable barrier of the Gulf of California. Still, unique haplotypes occur in the peninsula and the mainland, and peninsular populations are more structured than those on the mainland.

Origin and diversification of the saguaro cactus (Carnegiea gigantea): a within-species phylogenomic analysis

Reconstructing accurate historical relationships within a species poses numerous challenges, not least in many plant groups in which gene flow is high enough to extend well beyond species boundaries. Nonetheless, the extent of tree-like history within a species is an empirical question on which it is now possible to bring large amounts of genome sequence to bear. We assess phylogenetic structure across the geographic range of the saguaro cactus, an emblematic member of Cactaceae, a clade known for extensive hybridization and porous species boundaries. Using 200 Gb of whole genome resequencing data from 20 individuals sampled from 10 localities, we assembled two data sets comprising 150,000 biallelic single nucleotide polymorphisms (SNPs) from protein coding sequences. From these we inferred within-species trees and evaluated their significance and robustness using five qualitatively different inference methods. Despite the low sequence diversity, large census population sizes, and presence of wide-ranging pollen and seed dispersal agents, phylogenetic trees were well resolved and highly consistent across both data sets and all methods. We inferred that the most likely root, based on marginal likelihood comparisons, is to the east and south of the region of highest genetic diversity, which lies along the coast of the Gulf of California in Sonora, Mexico. Together with striking decreases in marginal likelihood found to the north, this supports hypotheses that saguaro's current range reflects post-glacial expansion from the refugia in the south of its range. We conclude with observations about practical and theoretical issues raised by phylogenomic data sets within species, in which SNP-based methods must be used rather than gene tree methods that are widely used when sequence divergence is higher. These include computational scalability, inference of gene flow, and proper assessment of statistical support in the presence of linkage effects.