Spatial phylogenetics of the native California flora

ABSTRACT. The deserts of southern California house a diverse and unique insect fauna. Velvet ants (Hymenoptera: Mutillidae) are common in these deserts. Velvet ants are important to ecosystem health, particularly in desert environments, because they are parasitic on the bees and wasps that help maintain overall ecosystem function. The goal of this study was to measure velvet ant diversity across the deserts of southern California, We made preliminary collections from 10 sites in a variety of areas in the western Sonoran Desert (Colorado Desert), the Mojave Desert, and the Great Basin Desert. We measured β-diversity using Sorensen's similarity index to compare velvet ant richness and relative abundance between different sites. To determine how accurate our similarity estimates were, and to gain an understanding of actual velvet ant diversity, we also compared velvet ant richness of 2 sites (Algodones Sand Dunes and Deep Canyon) using data obtained from the examination of museum specimens borrowed from over...

Understanding the relationships between taxonomic, functional, and phylogenetic diversity and endemism across environmental gradients is essential for elucidating the eco-evolutionary mechanisms that shape local plant communities. A database was compiled from field surveys, national herbarium records, and virtual records of perennial plant specimens collected in the aridity gradient of northern Chile, between 18 and 32°S. A large-scale dated phylogeny of available perennial plants was used, and 11 functional traits were selected to construct a dendrogram using the Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) method for the species present in our database. We calculated spatial patterns of a-diversity, including taxonomic (TD), functional (FD), and phylogenetic (PD) diversity, as well as weighted (WE), functional (FE), and phylogenetic (PE) endemism. We used multiscale geographically weighted regression (MGWR) to identify spatial congruencies and discrepancies among these dimensions and to test different eco-evolutionary processes. The diversity indices TD, FD and PD showed similar geographic patterns (R2 > 0.93), with lower diversity observed in absolute desert regions. The pattern of weighted endemism (WE) showed a weak association with functional endemism (FE) and phylogenetic endemism (PE) (local R2 < 0.48). The regions with lower FD or PD than expected given the TD (i.e. FD<TD and PD<TD) are mainly located in desert areas, as well as in high Andean areas influenced by the Atacama Desert, suggesting communities with associated in situ speciation processes, as well as a limitation of morpho-functional trait diversity in response to extreme environmental conditions (environmental filter hypothesis). Similarly, where FE and PE values are higher than expected given the WE (i.e. FE>WE and PE>WE), they are found in arid, high Andean and transitional zones, at different altitudes, which would indicate a greater presence of phylogenetic lineages and species with morpho-functional traits related to extreme environmental conditions and transitional biomes (arid-semiarid). These spatial discrepancies suggest different eco-evolutionary drivers between the dimensions of diversity and endemism (taxonomic, functional, and phylogenetic). Areas of high diversity and high endemism do not necessarily coincide, and both should be addressed by conservation efforts.

The geologic history of the outer continental margin (eugeoclinal) rocks in the El Paso Mountains and northern Mojave Desert has long been important in models for the development of the active continental margin in the western Cordillera. Current interpretations call for either strike-slip or thrust juxtaposition of eugeoclinal rocks against miogeoclinal/cratonal (platformal) rocks, or some combination of both strike-slip faulting and thrusting. Two broad and interrelated aspects of the history of the eugeoclinal rocks are at issue: (1) How much primary displacement is necessary to account for the present position of the eugeoclinal rocks? and (2) When were the eugeoclinal rocks thrust against platformal rocks? This study primarily addresses the second issue. Lithologic correlation indicates that the outcrop belt of eugeoclinal rocks is bounded by platformal rocks to the east and south. Platformal rocks are also present to the west, but many of these exposures restore to a position structurally beneath the eugeoclinal rocks when Tertiary extension is restored, implying stacking by a thrust. New U-Pb zircon geochronology and whole rock geochemistry and Sr, Nd, and Pb isotopic data for plutons in the El Paso Mountains and northern Mojave Desert lend insight into the timing of this thrusting. The outcrop belt of eugeoclinal rocks coincides with the only known Permian and Triassic plutons in the El Paso Mountains and northern Mojave Desert, which are dated at 260 to 240 Ma by U-Pb zircon in this report. Initial Sr and ϵ Nd(t) isotopic values from these plutons are distinct ≤0.704 and ≥+2, respectively) from continental lithosphere isotopic signatures ≥0.705 and ≤−2) of both Middle Jurassic plutons in the same area and Triassic plutons in the southern and eastern Mojave Desert. Feldspar common lead data for the Permian and Triassic plutons within the eugeoclinal outcrop belt also indicate limited crustal involvement and do not overlap previously reported values for common lead data from Mesozoic plutons in the eastern Mojave Desert region where Proterozoic basement is widespread. The observations and data reported here indicate that Late Permian–Early Triassic plutons in the northern Mojave Desert and El Paso Mountains were generated within or passed primarily through oceanic lithosphere, but later Jurassic plutons were derived from and/or interacted extensively with continental lithosphere. We hypothesize that the eugeoclinal rocks were deposited on oceanic crust that was thrust eastward over Precambrian cratonal basement and overlying strata between approximately 240 Ma and 175 Ma, a time of little documented tectonic activity in the Mojave Desert region. Postulated Permian or late Middle Jurassic east-directed thrusting is incompatible with our data and observations. The data also fill an important gap in palinspastic reconstructions of the early Mesozoic arc and indicate that this arc was northwest-trending and oblique to Paleozoic facies trends in the Mojave Desert.

Sand dunes in the Mojave and Great Basin Deserts are unique habitats that often harbor distinct and endemic taxa (Ricketts et al., 1999). Epps et al. (1998) compared sand dunes to ‘‘habitat islands’’ in the desert, which provide habitat for many sand-obligate organisms. Because many of these dunes are distant from other dunes, and often flanked by mountain ranges or alkaline hardpan, isolated populations of dune-restricted organisms are often genetically distinct (e.g., Britten and Rust, 1996; Epps et al., 1998). We attempted to discover phylogeographic patterns among populations of Colletes stepheni Timberlake, a sand dune restricted, oligolectic solitary bee. Colletes stepheni nests solely in loose sandy substrates and provisions its nest with pollen only from a limited number of plant species (Hurd and Powell, 1958; Minckley et al., 2000; Andrus, 2003). Populations of C. stepheni in the Mojave Desert use pollen only from Larrea tridentata (creosote bush; Zygophylaceae), which is a common shrub in the hot deserts of North America, while populations in the Great Basin Desert, a cold desert, use pollen from Psorothamnus (indigo bush; Fabaceae) (Andrus, 2003). Andrus (2003) attempted to find phylogeographic patterns among populations of C. stepheni from 13 dune sites across the Mojave and Great Basin Deserts using mtDNA. These attempts uncovered the presence of nuclear mitochondrial pseudogenes (NUMTS), which are mitochondrial genes that have been incorporated into the nuclear genome (Margulis, 1970). The presence of these pseudogenes in C. stepheni made the use of mtDNA for phylogeographic analyses difficult, if not impossible. While the majority of phylogeographic analyses use mtDNA, particularly the gene COI, to investigate phylogeographic patterns, several recent studies employ various nuclear genes to uncover intraspecific variation. For example, a phylogeographic study of sea urchins found that the internal transcribed spacer region 2 was more variable at the population level than COI (Iuri et al., 2007). Studies on several other taxa have also shown that the internal transcribed spacer regions 1 and 2 (ITS1 & ITS2) are variable at the population level (e.g., Mavarez et al., 2002; Gomez-Zurita and Vogler, 2003; Holderegger and Abbott, 2003). While nuclear genes are not widely used in phylogeographic studies of Hymenoptera, several recent studies have found population-level variation in various hymenopterans. For example, variation has been found among populations of stingless bees (De la Rua et al., 2007), an encyrtid wasp (Alvarez and Hoy, 2002), an oak gallwasp (Rokas et al., 2001), and several velvet ant species (Wilson and Pitts, 2008, 2009). Other studies on velvet ants (Hymenoptera: Mutillidae), while not specifically investigating intraspecific variation, showed that such variation exists in both the ITS1 and ITS2 sequences (Pilgrim and Pitts, 2006; Pitts et al., 2007; Pilgrim et al., 2008). Another nuclear gene, Long-wavelength rhodopsin (opsin), has not been widely used in population-level analyses, but has three introns (167 total bp in C. stepheni), which have been informative in differentiating between isolated populations of mutillid wasps (Wilson and Pitts, unpubl. data). Also, Almeida and Danforth (2009) in a phylogenetic analysis of colletid bees found that the introns of opsin were too variable to be used in a species-level analysis. This would suggest that the introns might be informative at the intraspecies level. Kuhlmann et al. (2007) found population-level differences in the introns of another nuclear gene Elongation Factor 1-Alpha for Colletes halophilus as well. In this study, we attempted to find phylogeographic patterns using three nuclear genes, the two rDNA internal transcribed spacer regions (ITS1 & ITS2), and the long-wavelength rhodopsin gene (Opsin).

Orchidaceae stands as one of the “flagship” groups in global biodiversity conservation, attracting significant attention from researchers in China. Previous studies have focused on taxonomic diversity, neglecting the integration of phylogeny and functional aspects. Here, we have leveraged a large dataset of distributions, evolutionary relationships, and functional traits of orchids in China to analyze geographic patterns of species richness (SR), weighted endemism (WE), phylogenetic diversity (PD), phylogenetic endemism (PE), functional diversity (FD), and functional endemism (FE). Furthermore, we analyzed the deviations between PD (or FD) and SR (PDdev, and FDdev), as well as between PE (or FE) and WE (PEdev, and FEdev), taking into account climatic and environmental variables. We also delineated the priority protection and survey areas of orchid plants in China. Our results revealed that the geographic patterns of SR, WE, PD, PE, FD, and FE for orchids generally exhibited similar trends. However, there were notable inconsistencies in the geographical patterns of PDdev, FDdev, PEdev, and FEdev, which might be related to the different environmental responses of these four diversity deviation metrics. We have pinpointed six priority conservation areas for orchids in China, i.e., southeasterrn Xizang, western Yunnan, central Yunan, the Karst area at the border of Guizhou and Guangxi, the border of Guangdong and Guangxi, and Taiwan Island. In addition, we have also identified certain priority survey areas for orchids, encompassing southeastern Xizang and other crucial locales. These findings will guide future conservation and research efforts aimed at safeguarding the rich biodiversity of orchids in China.

Aim Conservation is often prioritized by identifying regional clusters of threatened or endemic species. Another approach is to assess the evolutionary distinctiveness of groups of taxa using phylodiversity measures. However, quantification of evolutionary history has traditionally not accounted for its uneven geographical distribution due to the variation in species ranges. We assess the efficacy of phylogenetic endemism ( PE ) to predict high extinction risk in comparison to estimates of species range restriction (weighted endemism, WE ) and phylogenetic diversity ( PD ). PE measures the relative range restriction of evolutionary history (lineages), while WE concentrates on the tips of the tree of life, treating all such branches as being of equal length. Location/Methods Using New Zealand's endemic skinks and geckos, we mapped the geographical variation in their extinction risk, PE , WE and PD and measured the extent to which extinction risk exhibited phylogenetic clustering for each group. Correlations between geographical concentrations of high skink and gecko extinction risk with PE , WE and PD were calculated. Results PE was predictive of spatial clusters of high extinction risk for geckos ( r 2 = 0.34, P &lt; 0.001) while WE was markedly less so ( r 2 = 0.19, P &lt; 0.001). The reverse applied to skinks, with WE most predictive of high risk ( r 2 = 0.26, P &lt; 0.001). The phylogenetic signal of extinction risk was significantly conserved for geckos, but was weaker and non‐significant for skinks. PE and WE were not predictive of low risk. PD was not predictive of risk. Main conclusions PE and related measures may be predictive of extinction risk when risk is phylogenetically conserved. Mapping the geographical variation in PE could be a useful first assessment of extinction risk for many groups because phylogenies are increasingly available, while full risk status categories are not. These findings might apply to other groups and locations and warrant further investigation.

Aim To investigate the spatial patterns of species richness (SR), phylogenetic diversity (PD) and phylogenetic endemism (PE) in bycatch decapod crustaceans along the Brazilian Exclusive Economic Zone and to assess the influence of environmental variables and trawling effort on these diversity indices. Location Brazilian Exclusive Economic Zone. Taxa Decapoda. Methods We compiled bycatch occurrence data from peer‐reviewed studies and global biodiversity repositories. Diversity indices (SR, PD, PE, ED and WE) were estimated using a phylogenetic approach incorporating mitogenomic markers. Environmental and trawling effort data were extracted from global databases, and statistical analyses, including redundancy analysis (RDA), spatial regression and random forest models, were applied to determine the drivers of diversity. Results Decapod diversity showed strong spatial heterogeneity across the EEZ. SR peaked in southeastern Brazil in upwelling‐influenced ecotones, while PD and PE were highest in offshore and equatorial regions. PD was strongly associated with bottom temperature, primary productivity (PP) and current velocity; SR was mainly driven by salinity, light availability and PP; and PE was best explained by temperature and PP. Most hotspots of phylogenetic diversity and endemism fell outside Marine Protected Areas (MPAs), revealing significant conservation gaps in offshore and southern regions. Main Conclusions This study provides the first macroecological framework of decapod diversity in the Brazilian EEZ and one of the first applications of phylogenetic diversity (PD) and phylogenetic endemism (PE) metrics for decapods in the South Atlantic. We show that temperature, salinity, productivity and current dynamics differentially shape biodiversity metrics. Southeastern and offshore zones host unique evolutionary lineages but remain underrepresented in current MPA networks. By integrating phylogenetic and environmental data, our findings offer a baseline to improve spatial biodiversity assessments and support more representative conservation planning under shifting ocean conditions.

8 - The Desert Region

AimThe Mediterranean Basin is a major hotspot of plant biodiversity, including forest trees. Over the past centuries, Mediterranean forests have been fragmented and over‐exploited, to which the threats of climate change are now added. Our aim is to better understand patterns and processes of tree biodiversity in the Mediterranean and to provide indicators complementing the traditional approaches to biodiversity conservation based on species counts and occurrences, using georeferenced phylogenetic diversity and endemism analyses in a spatial ecological context.LocationMediterranean Europe.MethodsUsing a dated phylogeny of the 64 Euro‐Mediterranean tree genera, we calculated phylogenetic diversity for all 50 × 50 km2 grid cells spanning Mediterranean Europe (n = 643) and compared values with those obtained for genus‐level taxonomic diversity. Then, we tested the relative influence of geography, past and present climate, and soil on tree diversity (phylogenetic or taxonomic) and its geographical turnover. Geographical patterns of phylogenetic endemism were inferred using the Categorical Analyses of Neo‐ and Paleo‐Endemism (CANAPE) methodology.ResultsWe showed that phylogenetic and taxonomic diversity within and among cells are correlated and influenced by soil parameters as well as current, Holocene and Late Glacial Maximum climate. Southern Spain, Cyprus and some Aegean islands contained areas of disproportionately high phylogenetic diversity and a concentration of phylogenetic paleo‐endemics, while phylogenetic neo‐endemism was high in eastern Sicily. Mixed phylogenetic endemism regions were detected in southern Spain and Portugal, in the Balkans and in Crete.Main conclusionsOur phylogenetic approach provides relevant indicators for better protecting forests of the Mediterranean, encompassing past and present evolutionary processes and factors. We consider areas that show a concentration of evolutionary history manifested by high phylogenetic endemism as high priority targets for the conservation of the European tree flora.

Using complementary metrics to evaluate phylogenetic diversity can facilitate the delimitation of floristic units and conservation priority areas. In this study, we describe the spatial patterns of phylogenetic alpha and beta diversity, phylogenetic endemism, and evolutionary distinctiveness of the hyperdiverse Ecuador Amazon forests and define priority areas for conservation. We established a network of 62 one‐hectare plots in terra firme forests of Ecuadorian Amazon. In these plots, we tagged, collected, and identified every single adult tree with dbh ≥10 cm. These data were combined with a regional community phylogenetic tree to calculate different phylogenetic diversity (PD) metrics in order to create spatial models. We used Loess regression to estimate the spatial variation of taxonomic and phylogenetic beta diversity as well as phylogenetic endemism and evolutionary distinctiveness. We found evidence for the definition of three floristic districts in the Ecuadorian Amazon, supported by both taxonomic and phylogenetic diversity data. Areas with high levels of phylogenetic endemism and evolutionary distinctiveness in Ecuadorian Amazon forests are unprotected. Furthermore, these areas are severely threatened by proposed plans of oil and mining extraction at large scales and should be prioritized in conservation planning for this region.

AimIn this study, we explored spatial patterns of phylogenetic diversity (PD) and endemism in the flora of Norway and tested hypothesized post‐glacial environmental drivers of PD, including temperature, precipitation, edaphic factors and time since glacial retreat.LocationNorway.TaxonVascular plants (Trachaeophyta).MethodsWe produced a multi‐locus maximum‐likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate PD and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple‐model inference to identify environmental variables that contributed the most to the patterns of PD. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history.ResultsOur ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post‐glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterized by neo‐endemism, while the mild and wet regions were characterized by both paleo‐ and neo‐endemism. PD was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway.Main conclusionsBoth contemporary ecological factors (climate and habitat heterogeneity), and post‐glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.

ABSTRACTAimPoeciliids are ecologically important, are widely used as pets, and also have value as model organisms. To understand diversity within this family, we study their phylogenetic diversity (PD) at regional and local scales to delimit bioregions and identify patterns of biodiversity.LocationThe Americas.TaxonPoeciliidae (Actinopterygii: Cyprinodontiformes).MethodsWe expanded an existing dated phylogeny from 164 to 261 species with distributional data for 1o × 1o latitude × longitude cells (~111 km2) and conducted a cluster analysis (phylo‐jaccard distance) to delineate bioregions. For individual cells, we mapped species richness (SR), phylogenetic diversity (PD), weighted endemism (WE) and phylogenetic endemism (PE). We used randomisation tests to map phylogenetic clustering and over‐representation of short‐branch species by cell. We used categorical analysis of neo‐ and palaeo‐endemism to map neo‐, palaeo‐, mixed and super (mixed) endemism.ResultsWe delineated six bioregions. Highest regional species density and density of PD occurred on the Isthmus of Panamá (IOP). At the grid‐cell scale, the Grijalva–Usumacinta drainage is a hotspot for SR, PD, PE and WE; the IOP has high PD and PE; the Isthmus of Tehuantepec (IOT) has high PD, WE and moderately high SR; and western Hispaniola has high WE and moderately high SR. The Grijalva–Usumacinta drainage also includes cells of super (mixed) and palaeoendemism, while mixed endemism is widespread in Middle America and the Greater Antilles. Phylogenetic clustering is widespread, whereas over‐representation of short‐branch species is concentrated in the Chihuahuan Desert–Sierra Madre Oriental region and in western Hispaniola, both hotspots of neoendemism.Main ConclusionsWe found widespread diversification of genera intermixed with relict species (mixed endemism). Furthermore, SR and PD were strongly correlated. Centres of endemism include the Chihuahuan Desert–Sierra Madre Oriental, western Hispaniola, the IOT, the IOP and (most of all) the Grijalva–Usumacinta drainage. However, conservation efforts must occur within each bioregion and for each genus.

ABSTRACTA major challenge to biodiversity conservation is prioritizing species and regions for conservation under limited resources. Phylogenetic diversity (PD) and phylogenetic endemism (PE) together could provide an effective estimate for biodiversity conservation by identifying areas rich in evolutionarily unique lineages and range‐restricted evolutionary history that are in urgent need of protection. Furthermore, understanding the spatial patterns and environmental correlates of these phylogenetic metrices is crucial because it helps to uncover the underlying processes driving biodiversity. We used recently updated distributions and phylogenetic relationships of all Chinese lizards (~90%), and found that the PD and the PE hotspots are mainly located in southern China. We found that temperature plays a stronger role than precipitation, historical climatic stability and seasonality in shaping the spatial patterns of PD and PE. Additionally, PE tends to be higher in regions with greater heterogeneity. Based on the categorical analysis of neo‐ and paleo‐endemism, our results also indicated that the majority of PE hotspots (mix of neo‐ and paleo‐endemism) were located in mountainous terrain (e.g., Hengduan–Himalaya) and on islands (Hainan, Taiwan). Importantly, we show that these hotspots in Chinese mainland are mostly located outside protected areas. Overall, our study highlights these regions with high PD and PE are mainly in mountains of southern and northwestern China. However, current protected areas are insufficient for lizard conservation in China, as they do not adequately cover key centres of evolutionary history.

Phylogeography of Beck’s Desert Scorpion, Paruroctonus becki, reveals Pliocene diversification in the Eastern California Shear Zone and postglacial expansion in the Great Basin Desert

Herbivores are predicted to evolve appropriate mechanisms to process the plant secondary compounds (PSCs) in their diet, and these mechanisms are likely specific to particular suites of PSCs. Changes in diet composition over evolutionary time should select for appropriate alterations in metabolism of the more recent dietary components. We investigated differences in gene expression profiles in the liver with respect to prior ecological and evolutionary experience with PSCs in the desert woodrat, Neotoma lepida. This woodrat species has populations in the Mojave Desert that have switched from feeding on juniper to feeding on creosote at the end of the Holocene as well as populations in the Great Basin Desert that still feed on the ancestral diet of juniper and are naïve to creosote. Juniper and creosote have notable differences in secondary chemistry. Woodrats from the Mojave and Great Basin Deserts were subjected to a fully crossed feeding trial on diets of juniper and creosote after which their livers were analyzed for gene expression. Hybridization of hepatic mRNAs to laboratory rat microarrays resulted in a total of 20,031 genes that met quality control standards. We analyzed differences in large-scale patterns of liver gene expression with respect to GO term enrichment. Diet had a larger effect on gene expression than population membership. However, woodrats with no prior evolutionary experience to the diet upregulated a greater proportion of genes indicative of physiological stress compared with those on their natural diet. This pattern may be the result of a naïve animal's attempting to mitigate physiological damage caused by novel PSCs.