Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula,Mexico

Aim

Desert springs or oases are the only permanent mesic environments in highly water-limited arid regions. Oases have immense cultural, evolutionary and ecological importance for people and a high number of endemic and relic species. Nevertheless, they are also highly vulnerable ecosystems, with invasive species, overexploitation and climate change being the primary threats. We used the arthropod communities' spatiotemporal diversity and distribution patterns as a proxy to understand biodiversity dynamics in two geographically close but ecologically contrasting and highly threatened ecosystems: deserts and oases.

Location

Baja California Peninsula, Mexico.

Methods

Arthropod communities at five oases and surrounding desert scrub areas were sampled in two seasons. Using DNA metabarcoding and traditional taxonomic surveys, we tried to identify what biotic and abiotic characteristics of the habitat are important drivers of arthropod diversity and how these characteristics can change across spatial and temporal scales.

Results

Over 6200 individuals representing 23 orders were collected. In oasis samples, the community composition fluctuated more in space (i.e. among sites) than in time (i.e. seasons). Thus, seasonal changes did not affect oasis community diversity and composition, but the dissimilarity among sites increased with geographic distance. Moreover, anthropic activities negatively correlated with arthropod diversity in oases. On the other hand, the season, geography (e.g. latitude) and biotic characteristics of the habitat (e.g. sampled scrub species) significantly affected the diversity and composition of the desert arthropod communities.

Main Conclusions

Neutral dynamics (e.g. historical climatic events, dispersal limitation and spatial component) and human impact significantly influenced the biodiversity patterns of each oasis. In contrast, the habitat's seasonal variation and biotic characteristics were the most important variables influencing the diversity of the desert communities. Baja California oases harbour distinct invertebrate communities; therefore, each oasis should be conserved individually to preserve these unique assemblages.     

Molecular genetic analysis of two native desert palm genera,Washingtonia and Brahea,from the Baja California Peninsula and Guadalupe Island

The complex geological and ecological processes that have generated high levels of biodiversity and endemism in the Baja California Peninsula have been the subject of intensive study. However, relatively little is known about phylogeography of the iconic endemic palm species of this region. We therefore analyzed a total of 2,294 bp of chloroplast and 738 bp of nuclear sequence data in 169 samples of five native palm species from Baja California, Sonora and Guadalupe Island. We found that Washingtonia and Brahea palms had low levels of genetic diversity and were highly structured, with the majority of species and major geographic regions being characterized by distinct haplotypes. We also found strong support for currently recognized species in Washingtonia, but our results were less clear cut for Brahea due to haplotype sharing. Furthermore, patterns of population structure were broadly consistent with historical vicariant events such as the inundation of the Isthmus of La Paz, the formation of the Sea of Cortez, and the more recent colonization and isolation of Guadalupe Island's palms. Our findings contribute toward a growing appreciation of the complexity of plant responses to past geological changes and also provide valuable baseline genetic data on relict American palm species.     

Land use changes affect distributional patterns of desert birds in the Baja California peninsula, Mexico

Reliable plans for desert bird conservation will depend on accurate prediction of habitat change effects on their distribution and abundance patterns. Predictive models can help highlight relationships between human‐related and other environmental variables and the presence of desert bird species. Presence/absence of 30 desert bird species of Baja California peninsula was modelled on the basis of explanatory variables taken from the field, maps, and digital imagery. Generalized linear models were fit to each bird species using both variables representing human activity and other environmental factors as predictors that might influence distribution. Probability of species presence was used as a habitat suitability index to evaluate the effect of human activity when the model contained a significant human activity variable. No differences were found in bird species richness between natural sites and those transformed by agriculture or urbanization. Of 59 bird species recorded in surveys, 34% were positively or negatively associated with human‐transformed habitats. Fourteen species seem to benefit from transformation of natural vegetation by agriculture or urbanization, while six were negatively affected. Sensitivity analyses of final models indicated all were robust. Results suggest that the occurrence of a large percentage of bird species inhabiting scrub habitats is sensitive to human habitat transformation. This finding has important conservation implications at regional scale as fragmentation and conversion of desert ecosystems into agricultural and urban areas affect the distribution of species that are highly selective for scrub habitat. Land use and anthropogenic activities seem to change ecological patterns at large spatial scales, but other factors could drive species richness distribution too (i.e. individual species response, species–energy relationships). The spatial modelling approach at regional scale used in this study can be useful for designing natural resource management plans in the Sonoran desert scrub.     

Critique of parsimony analysis of endemicity as a method of historical biogeography

Aim Assess the value of parsimony analysis of endemism as either an a priori (cladistic) and an a posteriori (phylogenetic) method of historical biogeography. Location World‐wide. Methods Parsimony analysis of endemicity (PAE) and Brooks parsimony analysis (BPA). Results Parsimony analysis of endemicity is capable of finding correct and unambiguous area relationships only under scenarios of vicariance in combination with non‐response to vicariance or extinction. An empirical comparison between PAE and BPA, using the poeciliid fish genera Heterandria and Xiphophorus, demonstrates that PAE fails to document much of the historical complexity in this relatively simple system. Main conclusions The a priori assumptions of PAE are far more restrictive than those made by other a priori methods, limiting its utility as a method of cladistic biogeography. The inability of PAE to detect perfect vicariance or biogeographical histories involving dispersal, renders it unsuitable as a method of phylogenetic biogeography.     

Heavy Metal Accumulation in Four Species of Sea Turtles from the Baja California Peninsula, Mexico

Heavy metals were assessed in four species of sea turtles from the Baja California Peninsula, Mexico, representing the first report of heavy metal concentrations in tissues of post-yearling sea turtles from the Eastern Pacific. Concentrations of Cd measured in C. mydas kidney (653 μg/g dry wt) were the highest ever reported for any sea turtle species. Cd accumulated preferentially in kidney and the ratios of kidney to liver Cd in Baja California turtles were among the highest reported for sea turtles globally. Zn, Ni, and Mn concentrations were also significantly higher in kidney than other tissues, while Cu and Fe were greatest in liver, and all metals were lowest in muscle. With the exception of one value (69.9 μg/g in kidney of C. caretta), Pb was low in all tissues from Baja California. In comparisons across species, kidney of C. mydas had greater Zn and Ni concentrations as compared to other species, although there was no difference in liver metal levels among the species. Positive correlations were detected in the concentrations of Cd, Cu and Ni with the straight carapace length of C. caretta.     

Coccolithophorids from the west coast of Baja California, Mexico

Studies on coccolithophorids in Mexico are rather scarce, probably due to the use of traditional methods for studying marine phytoplankton (e.g. collection, preservation and analysis). This is the first study of the coccolithophorid flora from west coast of Baja California, Mexico. Bottle samples (4 l) were taken at various depths (5, 25 and 50 m), at fixed stations located on perpendicular transects along the west coast of Baja California, considering three different zones: North, Central and South. A total of 32 samples were studied by optical and scanning electron microscopy, yielding 24 taxa identified (17 species and 5 nominal varieties, plus 2 different varieties). The coccolithophorid assemblages are considered subtropical and coastal (with many cosmopolitan taxa). Emiliania huxleyi and Gephyrocapsa oceanica were the most abundant (relative abundance) and widespread species in the study area. We report 15 new records for the Mexican Pacific. The zonal and vertical distribution of some taxa are briefly discussed, as well as the taxonomy of Rhabdosphaera claviger, Helicosphaera carteri, H. hyalina and related taxa.     

Historical biogeography of the Yucatan Peninsula,Mexico: a perspective from ferns (Monilophyta) and lycopods (Lycophyta)

Based on known data sets and maximum entropy distribution data of fern and lycopod species registered in the Yucatán Peninsula, track and parsimony analyses were undertaken to evaluate the contribution of these groups to the establishment of biogeographical relationships of the peninsula with other areas. The resulting generalized tracks clearly agree with the geological origin of the peninsula and the previously recognized relationship with the Greater Antilles is not supported for ferns and lycopods. Instead, a Central American generalized track connects the Yucatán Peninsula with south‐eastern México and Central America. Floristically, the peninsula harbours 66 species of ferns and lycopods. Seven are registered for the first time in the Yucatán Peninsula and one is a new species for México. These species do not follow the latitudinal pattern expected if ecological factors, such as humidity and rainfall, were the most important in determining their distributions. Groups of areas recognized with parsimony analysis of endemicity could not be defined as provinces as a result of the lack of endemic species. Nevertheless, a regionalization scheme based on maximum entropy distribution data and supported by track analyses is proposed. Two separate districts are recognized within the Yucatán Peninsula: arid/dry Yucatán in the north and El Petén (humid) in the south. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 775–786.     

Dry vegetation in relation to the physical environment in the Baja California Peninsula,Mexico

Abstract. An ordination analysis of vegetation and flora of Los Cabos Region, Baja California Peninsula, Mexico and its relationships with their environment and geomorphic characteristics was studied at 38 sites, selected based on ecoregion mapping units (EMU) previously delineated for the study area. Multivariate methods were used to analyse the relationship between physical characteristics of the environment and the two primary vegetation types, the Dry tropical forest (DTF) and the Xerophilous scrubland (XS), which together represent 83% of the vegetation cover in the study area. Sites were grouped based on both physical characteristics and relative abundance of plant species. The results of the statistical analysis suggest that altitude, rainfall, temperature, and lithology can help explaining differences between these important vegetation types. In the case of XS, the morpho‐physiognomic characteristics of vegetation in each site discriminated between two scrub types.     

An annotated distributional checklist of the freshwater fish from Baja California Sur,México

An annotated distributional checklist of thefreshwater fish recorded historically andrecently in Baja California Sur, México, isprovided. This checklist is supported with4,857 specimens collected at freshwaterlocalities during the period of May 1991 toApril 2002, and complemented with a review ofspecimens in museums and in the literature. Thenative ichthyofauna is represented by 19species belonging to 16 genera and 12 families,with only two cases of endemism (Funduluslima and Gobiesox juniperoserrai). Thefirst occurrence of Centropomus viridisin freshwater environments of Baja Californiapeninsula is reported here. The familiesEleotridae and Mugilidae are the most diversewith 3 species each. Zoogeographically, most ofthe species are of tropical affinity(panamanian 63%, tropical amphiamerican 16%and circumtropical 5%) and of marineecological derivation (sporadic 53%,complementary 26%, vicarious 16% anddiadromous 5%). Six species are exotic in thisregion, of which Cyprinus carpio, Xiphophorus helleri and Tilapia cf. zilli are of recent introduction. The currentstatus of the endemic killifish (Funduluslima) is determined as endangered due tocompetition with Tilapia cf. zilliand other exotic fish.     

Application of parsimony analysis of endemicity in Amazonian biogeography: an example with primates

The distributions of 51 non-human primate species are used for Parsimony Analysis of Endemicity (PAE) to determine the relationships among 14 interfluvial regions in the Amazon basin, South America. Two most parsimonious cladograms were found. The strict consensus tree of these cladograms suggests an early separation between Lower Amazonia (eastern) and Upper Amazonia (western). The major clusters of interfluvial regions identified in the PAE cladogram are congruent with the areas of endemism delimited for birds. When interfluvial regions are converted into avian areas of endemism, the PAE cladogram is congruent with one of the two general areas cladograms suggested for Amazonia based on phylogenies of several clades of forest birds. Our analysis suggests that PAE can be used as a tool to objectively identify areas of endemism at an intra-continental scale as well as to make historical inferences. However, the value of a PAE cladogram in this latter application should be always evaluated by congruence with area cladograms built upon cladistic biogeography procedures.     

Element Concentrations in Some Species of Seaweeds from La Paz Bay and La Paz Lagoon, South-Western Baja California, Mexico

La Paz Bay and La Paz Lagoon are water bodies of the Gulf of California that are influenced by waste water discharges from the City of La Paz and from activities of the phosphorite mining company “Rofomex”. Because seaweeds concentrate elements from the water and are used as effective indicators of contamination by metals, we investigated their usefulness in this region. Concentrations of certain major elements (Ca, Fe, K and Na) and trace elements (As, Ba, Co, Cr, Cs, Hf, Rb, Sb, Sc, Se, Sr, Ta, Th, U, Zn and Zr) were determined in 12 species of seaweeds from La Paz Bay and La Paz Lagoon using instrumental neutron activation analysis. The contents of trace elements of environmental importance (As, Co, Cr, Fe, Sb, Se and Zn) in all studied samples are within the range of typical levels for a pristine environment not subjected to anthropogenic impact. Somewhat higher concentrations of Cr (81mg kg⁻¹), Hf (4mg kg⁻¹), Rb (48mg kg⁻¹), Sc (6.3mg kg⁻¹), Ta (0.95mg kg⁻¹), Th (6.8mg kg⁻¹), U (33mg kg⁻¹) and Zn (90mg kg⁻¹) were found in the green seaweed species Ulva (formerly Enteromorpha) intestinalis, whereas such elements as As (77mg kg⁻¹), Sb (1.4mg kg⁻¹) and Se (1.8mg kg⁻¹) were mainly concentrated in the species Sargassum sinicola, Codium cuneatum and Padina mexicana respectively. Because of their higher abundance and heterogeneity in elemental composition the seaweeds species Ulva intestinalis and Caulerpa sertularioides seem to be more suitable for further biomonitoring of heavy metal pollution of the coastal waters in this zone.     

Distribution patterns of the genus Pacifigorgia (Octocorallia: Gorgoniidae): track compatibility analysis and parsimony analysis of endemicity

Aim We analysed the distribution patterns of the eastern Pacific octocoral genus Pacifigorgia and deduced its ancestral distribution to determine why Pacifigorgia is absent from the Gulf of Mexico, the Caribbean of central America, and the Antilles. We also examined the current patterns of endemism for Pacifigorgia to look for congruence between hot spots of endemism in the genus and generally recognized areas of endemism for the eastern Pacific. Location The tropical eastern Pacific and western Atlantic, America. Methods We used track compatibility analysis (TCA) and parsimony analysis of endemicity (PAE) to derive ancestral distribution patterns and hot spots of endemism, respectively. Distributional data for Pacifigorgia were gathered from several museum collections and from fieldwork, particularly in the Pacific of Costa Rica and Panama. Results A single generalized track joined the three main continental eastern Pacific biogeographical provinces and the western Atlantic. This track can be included within a larger eastern Atlantic–eastern Pacific transoceanic track that may be the oldest transoceanic track occurring in the region. PAE results designate previously recognized eastern Pacific biogeographical provinces as Pacifigorgia hot spots of endemism. The number of endemic species, which for other taxonomic groups is similar among the eastern Pacific provinces, is higher in the Panamic province for Pacifigorgia. Main conclusions We propose that the absence of Pacifigorgia from the Gulf of Mexico, the Caribbean of central America, and the Antilles is the result of an ancient absence of the genus from these areas rather than the consequence of a major, recent, extinction episode. The Cortez province and the Mexican province appear together as a result of either non‐response to vicariance or dispersal across the Sinaloan Gap. We posit that the Central American Gap acts as a barrier that separates the Panamic province from the northern Cortez–Mexican province.     

Mycorrhizal characterization of the boojum tree, <Emphasis Type="Italic">Fouquieria columnaris</Emphasis>, an endemic ancient tree from the Baja California Peninsula,Mexico

The mycorrhizal association with the boojum tree, Fouquieria columnaris (=Idria columnaris), was studied. This unusual tree is almost exclusively endemic to granite and volcanic soils in highly arid areas of the Baja California Peninsula of Mexico. Soil and root samples from ten sites, covering the extent of geographic distribution of the tree on the peninsula, were analyzed. The roots of the boojum tree contained all structures of an arbuscular mycorrhizal (AM) association. Morphologically different species, 23 in number, were identified in close vicinity to the boojum tree indicating that F. columnaris is associated with a high number of AM species of several AM genera and families.     

Biological conservation of Isla de Cedros,Baja California,Mexico: assessing multiple threats

This paper gives a general overview of the biological conservation problems of Isla de Cedros, off the central part of the Pacific coast of the Baja California peninsula, Mexico. The island's conservation problems can be summarized as: lack of knowledge, habitat degradation, introduction of exotic species, overhunting, and (presumably) commercial capture of reptiles.     

Loureirophonte psammophila,a new species of Laophontidae T. Scott, 1904 (Copepoda: Harpacticoida) from Baja California,Mexico

Loureirophonte psammophila n. sp. was collected from coarse sediments of a beach near La Paz, Baja California, Mexico. The species belongs to the subterranea-group as defined by Fiers (1993). It differs from the other representative of the group, L. subterranea (Lang, 1965) in the presence of an outer dentiform process on 2nd segment of the antennula, the chaetotaxy of P.2–P.5 and the 1-segmented male endopodite P.4. A map with the distribution of the eleven species known so far is provided.     

Distributional modelling and parsimony analysis of endemicity of Senecio in the Mediterranean-type climate area of Central Chile

Aim Floristic blocks and areas of endemism resulting from a parsimony analysis of endemicity (PAE) using raw floristic data versus data generated from distributional modelling for 130 species in the genus Senecio Tourn. ex L. distributed in the Mediterranean‐type climate area of Central Chile were compared, and the results were used to identify conservation priorities for the flora of the region. Location Central Chile, between 30° and 38° S. Methods Using herbarium records, a species × area matrix consisting of presence/absence data was constructed from a 0.5° × 0.5° grid. Distributional modelling techniques incorporating vegetation formations, elevation and the contagion index were used to interpolate floristic composition of poorly known areas. Parsimony analysis of endemicity was used to identify floristic blocks and areas of endemism. Results Using the number of most parsimonious trees as an index, distributional modelling greatly optimized the results of the PAE analysis. Three floristic blocks and four areas of endemism were suggested based on the PAE results using potential distribution data not incorporating the contagion index, while four blocks and two areas of endemism were suggested from the PAE results using potential distribution data incorporating the contagion index. Floristic blocks for the northern coast, southern Andes, and northern/central Andes were found, with some blocks showing divisions within them representing distinct geographic subunits. Major breaks between and within floristic blocks were identified at 32.5°–33° S and 34.5°–35° S. Main conclusions The floristic blocks identified with the distributional modelling and PAE correspond well to results from some previous studies and support hypothesized biogeographic divisions within Central Chile. The results were similar to those obtained from parallel analysis of the entire tree flora of Central Chile. The vegetative formation‐based distributional modelling produced robust and reproducible results when used along with PAE, especially when the contagion index was incorporated, and is a useful technique for area classification. The results demonstrate the utility of Senecio as an indicator genus for biogeography and conservation in southern South America.     

Contributions toward understanding the biodiversity of Passiflora in North America: Updates and a new combination from the Baja California Peninsula,Mexico and vicinity

The Baja California Peninsula and surrounding landmasses harbor an abundant flora in an otherwise harsh and arid environment. Of the many plant groups native to this peninsular and insular region, passionflowers (Passiflora, Passifloraceae) are represented by several conspicuous taxa that all belong to a single lineage, section Dysosmia. Basic questions remain regarding this group, particularly the taxonomic status among the Passiflora arida complex. Therefore, we investigated the claims of endemism, habitat characteristics, and taxon boundaries with in section Dysosmia in the Baja California region using extensive sampling of herbarium specimens and iNaturalist observations. We confirmed that only one of the native Passiflora taxa (P. fruticosa) was endemic to the Baja California Peninsula, with an additional taxon (P. palmeri) considered near‐endemic. Environmental data revealed significant distinctions between the habitats of many of the native taxa as well as within the P. arida complex, especially with respect to precipitation and temperature tolerances. Geometric morphometric analyses of leaf shape were largely not successful at separating taxa, indicating leaf shape may not be a good indicator of taxon identity in this particular group. Based on ecological differences and discrete macro‐ and micromorphological features, a varietal name is here synonymized and a new combination is proposed: Passiflora pentaschista.     

Phylogenetic structure among pocket gopher populations,genus Thomomys (Rodentia: Geomyidae), on the Baja California Peninsula

We determined the phylogenetic relationships, population history, and hierarchical structure of genetic variation in pocket gophers distributed on the Baja California Peninsula (BCP), based on extensive geographic sampling. Using a fragment of the mitochondrial gene cytochrome b (cyt b), we found three latitudinal structured geographic clades (northern, central, and southern). The northern clade occurs in the border area of the USA and the north of BCP, the central clade occurs from the peninsular highlands through the Central Desert of Baja California, and the southern clade is distributed south of the San Ignacio Lagoon. AMOVA showed that genetic variation is higher among clades (64%) than within populations (18.1%). The deepest divergence among clades is very shallow (～300 000 years), which suggests that climatic changes during the Pleistocene or some inhospitable habitats have affected the structure of this group, rather than influences from older marine transgressions. Phylogenetic groups disclosed by our results do not coincide with the current infraspecific classification; therefore, we propose a change of epithet for BCP gophers (Thomomys nigricans) and a new subspecific taxonomic arrangement with four subspecies: Thomomys nigricans anitae, Thomomys nigricans martirensis, Thomomys nigricans nigricans, and Thomomys nigricans russeolus. © 2013 The Linnean Society of London     

Biogeographic analysis of endemic cacti of the Sierra Madre Oriental, Mexico

The distribution of cacti species that inhabit the Sierra Madre Oriental (SMO) was analysed. Grid-cells were analysed using parsimony analysis of endemicity (PAE) and endemism indices. Areas characterized by their diagnostic species were determined, aiming to propose areas for the conservation of threatened cacti. Distributional data were obtained from 1936 herbarium specimens, electronic information, and from field collections. Eight areas of endemism and three main clades were obtained from the grid-cell analysis. Areas obtained from the endemism indices are very similar to those obtained with the PAE, but differ in the association of grid-cells. PAE showed endemism patterns indicating that southern and central sections of the SMO province are the areas richest in geographically-restricted species. The results obtained with different endemism indices detected more or less the same areas, although the importance level is different. The corrected weighted endemism index can be considered as a reliable measure of endemism because it is unrelated to species richness. A regionalization of the SMO in three subprovinces is suggested, supported by characteristic cacti taxa and the existence of natural barriers.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 373–389.     

Biogeography and endemism of ants (Hymenoptera: Formicidae) in Baja California, Mexico: afirst overview

Abstract Aims Ants (Hymenoptera: Formicidae) of the Baja California peninsula are poorly known, with information based largely on scattered museum and literature records. We provide the first comprehensive account of ant species occurring on the peninsula, we examine distribution patterns, and we assess the ‘peninsular effect’ which predicts that species richness declines from the base to the tip of a peninsula. Location Peninsula of Baja California, Mexico. Methods Data collection involved examining, identifying and recording label data from c. 2350 series of ants. These records provide a provisional, if incomplete, species list. We applied the incidence‐based estimator, Chao‐2, to our data base of specimen records to estimate the total number of ant species on the peninsula. We assessed endemism by comparing our peninsular species list to those from adjacent states. The peninsular effect was tested by comparing genus and species level richness between the two states of Baja California, and across five latitudinal blocks. Results We document 170 native ant species in thirty‐three genera, plus six non‐native species, in Baja California. It seems likely that additional species remain to be discovered: the Chao‐2 estimator of species richness, at 206.0 species, is about 20% higher than our observed species richness. About 30% of the species and 20% of the genera are restricted within Baja California to the relatively mesic California Floristic Province of north‐western Baja California. Nearly all of these species also occur in California. Forty‐seven species (27.6%) are peninsula endemics. Using our entire data set, the peninsular effect appears to be strong, with about twice as many species in the northern state of Baja California than are recorded from the southern state of Baja California Sur; the ratio of genera is 33 to 24. However, this effect becomes weak at the species level and absent at the genus level when minimizing habitat effects by omitting species restricted to the California Floristic Province. At a finer scale, across latitudinal blocks of about 1.9°, the number of species declines towards central portions of the peninsula and then increases in the Cape Region. Nine ant species display strongly disjunct distributions, and these occur in two general patterns: peninsula disjuncts and peninsula–mainland disjuncts. Main conclusions The Baja California peninsula supports a diverse and distinctive ant fauna, with the proportion of endemic species similar to that displayed by plants. Patterns of species and genus richness across the five latitudinal blocks provide poor support for the peninsular effect. Moreover, habitat diversity, especially that related to topographic relief, appears to be the most important factor affecting the gradient of ant species richness in Baja California. Additional collections are needed to develop a more complete species list and to determine the boundaries and status of many species. Nevertheless, the present data base provides a useful starting point for understanding the evolution of ant assemblages in Baja California and for comparison with peninsular patterns in other taxa.