A protocol for temporal calibration of general area cladograms

Aim To describe a protocol for incorporating a temporal dimension into historical biogeographical analysis, while maintaining the essential independence of all datasets, involving the generation of general area cladograms. Location Global. Methods General area cladograms (GACs) are a reconstruction of the evolutionary history of a set of areas and unrelated clades within those areas. Nodes on a GAC correspond to speciation events in a group of taxa; general nodes are those at which multiple unrelated clades speciate. We undertake temporal calibration of GACs using molecular clock estimates of splitting events between extant taxa as well as first appearance data from the fossil record. We present two examples based on re‐analysis of previously published data: first, a temporally calibrated GAC generated from secondary Brooks parsimony analysis (BPA) of six extant bird clades from the south‐west of North America using molecular clock estimates of divergence times; and second, an analysis of African Neogene mammals based on a phylogenetic analysis for comparing trees (PACT) analysis. Results A hypothetical example demonstrates how temporal calibration reveals potentially critical information about the timing of both unique and general events, while also illustrating instances of incongruence between dates generated from molecular clock estimates and fossils. For the African Neogene mammal dataset, our analysis reveals that most mammal clades underwent geodispersal associated with the Neogene climatic optimum (c. 16 Ma) and vicariant speciation in central Africa correlated with increased aridity and cooler temperatures around 2.5 Ma. Main conclusions Temporally calibrated GACs are valuable tools for assessing whether coordinated patterns of speciation are associated with large‐scale climatic or tectonic phenomena.     

A trait-based approach to assess niche overlap and functional distinctiveness between non-indigenous and native species

Our understanding of the community assembly processes acting on non-indigenous species (NIS), as well as the relationship with native species is limited, especially in marine ecosystems. To overcome this knowledge gap we here develop a trait-based approach based on the functional distinctiveness metric to assess niche overlap between NIS and native species, using high-resolution data on benthic invertebrate communities in the Baltic Sea. Our results show that NIS retain a certain degree of similarity with native species, but display one or a few singular unique traits (e.g., bioturbation ability). Furthermore, we demonstrate that community assembly processes, including both environmental filtering and limiting similarity affect NIS establishment, but that their effects may be highly context dependent, as illustrated by pronounced spatial patterns in distinctiveness. Finally, our trait-based approach provides a generic framework applicable to other areas and organisms, to better understand and address biological invasions.     

Older than New Caledonia emergence? A molecular phylogenetic study of the eneopterine crickets (Orthoptera: Grylloidea)

Aim A New Caledonian insect group was studied in a world‐wide phylogenetic context to test: (1) whether local or regional island clades are older than 37 Ma, the postulated re‐emergence time of New Caledonia; (2) whether these clades show evidence for local radiations or multiple colonizations; and (3) whether there is evidence for relict taxa with long branches in phylogenetic trees that relate New Caledonian species to geographically distant taxa. Location New Caledonia, south‐west Pacific. Methods We sampled 43 cricket species representing all tribes of the subfamily Eneopterinae and 15 of the 17 described genera, focusing on taxa distributed in the South Pacific and around New Caledonia. One nuclear and three mitochondrial genes were analysed using Bayesian and parsimony methods. Phylogenetic divergence times were estimated using a relaxed clock method and several calibration criteria. Results The analyses indicate that, under the most conservative dating scenario, New Caledonian eneopterines are 5–16 million years old. The largest group in the Pacific region dates to 18–29 Ma. New Caledonia has been colonized in two phases: the first around 10.6 Ma, with the subsequent diversification of the endemic genus Agnotecous, and the second with more recent events around 1–4 Ma. The distribution of the sister group of Agnotecous and the lack of phylogenetic long branches in the genus refute an assumption of major extinction events in this clade and the hypothesis of local relicts. Main conclusions Our phylogenetic studies invalidate a simple scenario of local persistence of this group in New Caledonia since 80 Ma, either by survival on the New Caledonian island since its rift from Australia, or, if one accepts the submergence of New Caledonia, by local island‐hopping among other subaerial islands, now drowned, in the region during periods of New Caledonian submergence.     

Evidence and hypothesis in biogeography

Evidence can provide support for or against a particular biogeographical hypothesis. Treating a hypothesis as if it were evidence or an empirical observation confounds many biogeographical analyses. We focus on two recent publications that address, in part, the evolution of the biota of Sulawesi, the large Indonesian island in the centre of the Indo‐Australian Archipelago. Many biogeographical explanations are hampered by invoking simple notions of mechanism or process – dispersal and vicariance – or constraints, such as dispersal from a centre of origin, and, in so doing, dismiss more complex geological phenomena such as emergent volcanoes within island chains or composite areas as irrelevant. Moreover, they do not search for, therefore never discover, biogeographical patterns that may better explain the distribution of biota through time.     

Phylogeography sheds light on the central–marginal hypothesis in a Mediterranean narrow endemic plant

Background and Aims

Understanding the factors that shape variation in genetic diversity across the geographic ranges of species is an important challenge in the effort to conserve evolutionary processes sustaining biodiversity. The historical influences leading to a central–marginal organization of genetic diversity have been explored for species whose range is known to have expanded from refugia after glacial events. However, this question has rarely been addressed for Mediterranean endemic plants of azonal habitats such as rocky slopes or screes. In this context, this comprehensive study examined molecular and field data from Arenaria provincialis (Caryophyllaceae), a narrow endemic plant of south-eastern France.

Methods

Across the whole geographic range, an investigation was made of whether high levels of abundance and genetic diversity (estimated from amplified fragment length polymorphism markers) are centrally distributed, to evaluate the relevance of the central–marginal hypothesis. Phylogeographic patterns inferred from chloroplast DNA (cpDNA) were used, applying Bayesian methods to test the influence of past biogeographic events. Multivariate analysis combining phylogeographic and ecological data was used to reveal the historical and ecological distinctiveness of populations.

Key Results

Despite the narrow distribution of A. provincialis, a high level of nucleotide variation is found within cpDNA loci, supporting its persistence throughout the Pleistocene period. The area characterized by the highest genetic diversity is centrally located. Structured phylogeography and Bayesian factor analysis supported the hypothesis that the central area of the distribution was the source of both westward and eastward migrations, probably during arid periods of the Pleistocene, and more recently was a crossroads of backward migrations. By contrast, the two areas located today at the range limits are younger, have reduced genetic diversity and are marginal in the ecological gradients.

Conclusions

This study highlights a case of strong population distinctiveness within a narrow range. Phylogeography sheds light on the historical role of the areas centrally situated in the distribution. The current range size and abundance patterns are not sufficient to predict the organization of genetic diversity.     

Vom Ruhr Zoo zur ZOOM Erlebniswelt III: Der Bauabschnitt Asien

In the Zoom Erlebniswelt Gelsenkirchen the third and last biogeographical area dedicated to the Asian fauna was opened in March 2010 covering a total area of five hectares. In May 2013 a new enclosure for tigers was added. The emphasis of the Asia area lies on a 4700 m² tropical hall with mammals and birds, and Asian gastronomic facilities as well. Included is a mixed species exhibit for orangutans (Pongo abelii), northern plains grey langurs (Semnopithecus entellus) and Asian small clawed otters (Aonyx cinerea). Along a 1.3 km outside path enclosures for some species of colder climates were built, too. The transformation of the former Ruhr Zoo Gelsenkirchen to the modern ZOOM Erlebniswelt herewith is brought to a close.     

Habent Fata Sua: The Rise and Fall of Garden Plants

Background: Rare cactus in the Americas and other species worldwide are threatened species because of their high level of habitat specialisation, narrow distribution range and continuing population decline.

Aims: To identify management units (MUs) based on genetic variability and demographic structure in order to propose assertive conservation actions for Mammillaria crucigera and to provide a model case study for other species that are under similar threats.

Methods: We genotyped through eight microsatellite loci in 171 individuals and described demographic structures in six populations of this cactus based on plots of 1 m².

Results: Across populations with a mean density of 2.6 m^?2 and a total of ~500 individuals counted, 30% of the individuals were reproductive (diameter >2 cm). The total heterozygosity was low (H_O = 0.54), but the inbreeding coefficient (F_IS = 0.29) and the allele diversity (N_A = 20) were high. Four genetic groups were distinguished, although considering the demographic structure, we propose three MUs.

Conclusions: It is critical to maintain the genetic connectivity within and among MUs, which can only be achieved through cooperation between government authorities and local habitants to halt the degradation and further destruction of the remnant populations. Searching MUs allows the identification of critical areas for conservation issues for all species whose extant populations are in a fragmented landscape.     

Vocal Cues to Identity: Pied Babblers Produce Individually Distinct But Not Stable Loud Calls

The ability to identify social partners can play a key role in the coordination of social behaviours in group‐living animals. Coordinating social behaviours over long distances becomes problematic, as cues to identity are often limited to one or two sensory modalities. This limitation can often select for strong individuality in those cues used for long‐distance communication. Pied babblers, Turdoides bicolor, produce a number of different types of ‘loud calls’ which are frequently used to signal to individuals beyond the range of visual or olfactory pathways of communication. Here, we show that three of these ‘loud call’ types, the v‐shaped chatter, the double note ascending chatter and the atonal chatter, are each individually distinct. We hypothesise that individuality in the three loud call types tested here may represent a possible pathway to social recognition in this species that may have important consequences for social interactions. However, we also found that the atonal chatter was unstable between years suggesting that this particular call type may not be a reliable long‐term indicator to identity which may affect long‐term recognition in this species.