Ella Vázquez-Domínguez

The tropics: cradle, museum or casino? A dynamic null model for latitudinal gradients of species diversity.

Several ecological and evolutionary hypotheses have been proposed to explain the latitudinal diversity gradient (LDG), but a general model for this conspicuous pattern remains elusive. Mid-domain effect (MDE) models generate gradients of species diversity by randomly placing the geographic ranges of species in one- or two-dimensional spaces, thus excluding both evolutionary processes and the effect of contemporary climate. Traditional MDE models are statistical and static because they determine the size of ranges either randomly or based on empirical frequency distributions. Here we present a simple dynamic null model for the LDG that simulates stochastic processes of range shifts, extinction and speciation. The model predicts higher species diversity and higher extinction and speciation rates in the tropics, and a strong influence of range movements in shaping the LDG. These null expectations should be taken into consideration in studies aimed at understanding the many factors that generate latitudinal diversity gradients.

Phylogenetic analysis of nuclear and mitochondrial DNA reveals a complex of cryptic species in Crassicutis cichlasomae (Digenea: Apocreadiidae), a parasite of Middle-American cichlids.

We obtained nuclear ITS-1 and mitochondrial cox1 sequences from 225 Crassicutis cichlasomae adults collected in 12 species of cichlids from 32 localities to prospect for the presence of cryptic species. This trematode is commonly found in species of cichlids over a wide geographic range in Middle-America. Population-level phylogenetic analyses of ITS-1 and cox1, assessments of genetic and haplotype diversity, and morphological observations revealed that C. cichlasomae represents a complex of seven cryptic species for which no morphological diagnostic characters have been discovered thus far. Bayesian and Maximum Likelihood analyses of concatenated datasets (906 bp) recovered eight lineages of C. cichlasomae, all with high posterior probabilities and bootstrap branch support. Values of genetic divergence between clades ranged from 1.0% to 5.2% for ITS-1, and from 7.2% to 30.0% for cox1. Morphological study of more than 300 individuals did not reveal structural diagnostic traits for the species defined using molecular evidence. These observations indicate that some traditional morphological characters (e.g., testes position) have substantial intra-specific variation, and should be used with caution when classifying C. cichlasomae and their sister taxa. Additionally, phylogenetic analyses did not reveal a strict correlation between these cryptic species and their host species or geographic distribution, however it appears that genetic distinctiveness of these cryptic species was influenced by the diversification and biogeographical history of Middle-American cichlids.

Living on the edge: roads and edge effects on small mammal populations

1. Roads may affect wildlife populations through habitat loss and disturbances, as they create an abrupt linear edge, increasing the proportion of edge exposed to a different habitat. Three types of edge effects have been recognized: abiotic, direct biotic, and indirect biotic. 2. We explored the direct biotic edge effects of 3- to 4-m wide roads, and also a previously unrecognized type of edge effect: social. We live-trapped two threatened endemic rodents from Cozumel Island (Oryzomys couesi cozumelae and Reithrodontomys spectabilis) in 16 plots delimited by roads on two sides, to compare edge effects between two adjacent edges (corners), single-edge and interior forest, on life history and social variables. 3. No significant edge effects were observed on the life-history variables, with the exception of differences in body condition between males and females of O. c. cozumelae near edges. Both species showed significant and contrasting effects on their social variables. 4. O. c. cozumelae was distributed according to its age and sex: the proportion of adults and males was higher in interior than near edges, while juveniles and females were more abundant near edges. More nonreproductive females were present in corners than in single-edge and interior, while the opposite distribution was observed for nonreproductive males. 5. The distribution of R. spectabilis was related to its age and reproductive condition, but not to its sex. The proportion of adults was significantly higher in corners, while juveniles were only caught in single-edge and interior quadrants. The proportion of reproductive individuals was higher in edge than interior quadrants, while reproductive females were only present in edge quadrants. 6. We found significant differences between the quadrants with the greatest edge exposure in comparison with other quadrants. The social edge effects we identified complement the typology of edge effects recognized in ecological literature. Our study provides insight into the effects that sharp road edges have on biological and social characteristics of small mammal populations, highlighting how such effects vary among species. Our findings have important conservation implications for these threatened species, but are also applicable in a broader context wherever there are abrupt edges caused by linear landscape features.

Extirpation of an insular subspecies by a single introduced cat: the case of the endemic deer mouse Peromyscus guardia on Estanque Island, Mexico

The Angel de la Guarda deer mouse Peromyscus guardia on Estanque Island, in the Angel de la Guarda archipelago of the Gulf of California, was probably driven to extinction by a single introduced domestic cat. P. guardia was trapped on the island in October 1995, at which time the species was still relatively abundant. In 1998 a domestic cat was spotted on the island; no deer mice were found at that time nor during subsequent field work in 1999 and 2001. In 1998, c . 100 cat scats were collected, 2% of which contained P. guardia bone remains and 90% P. guardia hair. The cat, which was eradicated in 1999, was the only introduced predator on the island. Our results confirm the extreme vulnerability of island rodent populations to the introduction of alien mammalian predators. To our knowledge, apart from the extermination of Stephens Island wren Xenicus lyalli in New Zealand in 1894 by the lighthouse keepers cat, this is the first report of the destruction of the total population of an insular species by a single cat. With two of the three subspecies of P. guardia now extinct the only potentially extant population is on the larger Angel de la Guarda Island, where the species was last seen in 1991. A comprehensive survey of the island is required, with subsequent action for the species recovery and conservation if it is found to be extant.

Implications of the Hierarchical Structure of Biodiversity for the Development of Ecological Indicators of Sustainable Use

Abstract The increasing interest, and the actual necessity, for adequate means to evaluate how sustainable human activities are, has led to efforts to define indicators of sustainability. We propose the use of ecological indicators of sustainability that take into account the hierarchical structure of biodiversity, distinguishing composition, structure and function at the different levels of biological organization: ecosystem and landscape, community, and population and genetic levels. We evaluated the advantages of selecting and combining indicators of different hierarchical levels by examining several use and management projects. Examples of transformed land like large-scale plantations, perform well when evaluated by ecosystem-level indicators, but lead to neglect of some composition and structure components if evaluated at different levels. Limitations in using a small number of indicators become evident in cases of intensive exploitation of resources, such as the extractive reserves, which yield good results under the ecosystem and community levels, but fail under the population and genetic indicators. Wild species management, a common example of the use of population-level indicators, do not perform well under other indicators at broader scales. We also reviewed projects that are sustainable at different hierarchical levels, like some multispecific exploitation forestry management, in which harvesting of resources is at or below sustainable levels, selective extraction is performed, and where natural regeneration and recruitment of species is allowed. It is evident that the adequacy of indicators is not universal and must take into account the complexity of processes and variables involved in the different biological levels and human components, highlighting possible conflicts and contradictions, while increasing knowledge about maintenance of quality in the use and exploitation of resources that the relevant stake-holders regard as important.

Understanding and monitoring the consequences of human impacts on intraspecific variation

Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill‐advised because phenotypic and genetic variations within and among populations can have dramatic effects on ecological and evolutionary processes, including responses to environmental change, the maintenance of species diversity, and ecological stability and resilience. At the same time, environmental changes associated with many human activities, such as land use and climate change, have dramatic and often negative impacts on intraspecific variation. We argue for the need for local, regional, and global programs to monitor intraspecific genetic variation. We suggest that such monitoring should include two main strategies: (i) intensive monitoring of multiple types of genetic variation in selected species and (ii) broad‐brush modeling for representative species for predicting changes in variation as a function of changes in population size and range extent. Overall, we call for collaborative efforts to initiate the urgently needed monitoring of intraspecific variation.

Using DNA barcoding to link cystacanths and adults of the acanthocephalan Polymorphus brevis in central Mexico

In parasitic organisms, particularly helminths, the usage of the mitochondrial cytochrome c oxidase subunit I gene as the standard DNA barcoding region for species identification and discovery has been very limited. Here, we present an integrated study, based on both DNA barcoding and morphological analyses, for acanthocephalans belonging to the genus Polymorphus, whose larvae (cystacanths) are commonly found in the mesentery of freshwater fishes, while adults are found in the intestine of fish‐eating birds. The alpha taxonomy of parasitic helminths is based on adult morphological traits, and because of that larval forms cannot be identified to species level based on morphology alone. DNA barcoding offers an alternative tool for linking larval stages of parasitic organisms to known adults. We sequenced cystacanths collected from freshwater fishes in localities across central Mexico and adults obtained from fish‐eating birds, to determine whether they were conspecific. To corroborate the molecular results, we conducted a morphometric analysis with ‘Proboscis profiler’, which is a software tool developed to detect heterogeneity in morphologically similar acanthocephalans based on the multivariate statistical analysis of proboscis hook dimensions. Both sources of information indicate that cystacanths infecting freshwater fishes in central Mexico belong to a single species, Polymorphus brevis.

Molecular systematics of Batrachoseps (Caudata, Plethodontidae) in southern California and Baja California: Mitochondrial-nuclear DNA discordance and the evolutionary history of B. major

Inferences about species boundaries and evolutionary history are often complicated by discordance between datasets. In recent times, considerable effort has been devoted to understanding the causes of discordance between the patterns of genetic variation and structure shown by different unlinked molecular markers. The genus Batrachoseps (Caudata, Plethodontidae), the most diverse group of salamanders in western North America, is characterized by limited morphological variation and discordance between molecular datasets, making it a challenging group for taxonomists but also a good model to test newly developed analytical methods to sort out possible sources of discordance. In this study, we present a comprehensive assessment of the evolutionary history of B. major, one of the most widespread species in the genus, based on extensive sampling and phylogenetic and coalescent analyses of data from mitochondrial and nuclear markers. We found non-monophyly of mtDNA in B. major, with two lineages (northern and southern) that are more closely related to other species in the genus than to each other, but this division was not apparent in nuclear DNA. Despite non-monophyly in gene trees, species tree analyses recovered a sister group relationship between the two lineages of B. major, and coalescent simulations suggested that there is no need to invoke gene flow to account for the discordance across gene trees. The possibility that these two lineages represent sister, cryptic taxa, is discussed in the context of Bayesian methods of species/lineage delineation. Contrary to prior expectations, B. major has experienced extensive diversification on the Baja California Peninsula, where four endemic lineages have persisted for at least 4 million years.

Comparative Phylogeography: Designing Studies while Surviving the Process

Comparative phylogeography (CP) can be defined as the study of the effects of evolutionary history and biogeography on the distribution of genetic variation of codistributed species. CP studies have intensified in recent years, which is a natural progression from an extensive history of intraspecific phylogeography research. On the basis of a thorough review of published studies that specifically deal with CP, our objective in the present review is to provide a comprehensive guide to the discipline that will help those wishing to develop a CP project. We describe the characteristics that shape a CP study and summarize the fields prime theoretical, methodological, and analytical requirements; frequent hypotheses tested; and current achievements and limitations, including a variety of illustrative examples throughout. We finally highlight some new approaches in CP and briefly discuss future directions for the field.

Ancient DNA and the tropics: a rodent's tale

Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as Ototylomys phyllotis, found in Holocene and Late Pleistocene stratigraphic layers from Loltún, a humid tropical cave located in the Yucatan peninsula. We extracted DNA and amplified six short overlapping fragments of the cytochrome b gene, totalling 666 bp, which represents an unprecedented success considering tropical ancient DNA samples. We performed genetic, phylogenetic and divergence time analyses, combining sequences from ancient and modern O. phyllotis, in order to assess the ancestry of the Loltún samples. Results show that all ancient samples fall into a unique clade that diverged prior to the divergence of the modern O. phyllotis, supporting it as a distinct Pleistocene form of the Ototylomys genus. Hence, this rodents tale suggests that the sister group to modern O. phyllotis arose during the Miocene–Pliocene, diversified during the Pleistocene and went extinct in the Holocene.