Reconstructing ancestral ranges in historical biogeography: properties and prospects

Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.     

Are diminutive turtles miniaturized? The ontogeny of plastron shape in emydine turtles

Miniaturization, or the evolution of a dramatically reduced body size compared to related lineages, is an extraordinarily widespread phenomenon among metazoans. Evolutionary biologists have been fascinated by miniaturization because this transition has occurred numerous times, often among close relatives, providing a model system for studying convergent evolution and its underlying mechanisms. Much of the developmental work describing the ontogeny of miniature species suggests that paedomorphosis is the predominant avenue of miniaturization. Nevertheless, specific alterations to ontogeny appear highly variable, so that even related lineages with similar miniaturized traits produce those similarities via distinct ontogenetic paths. One major vertebrate group that has been overlooked in research on miniaturization is turtles. In the present study, we examined patterns of shape change in the plastron (the ventral part of the shell) over the course of ontogeny in a small clade of turtles (Emydinae) aiming to investigate whether two independently evolved diminutive members of the clade (Glyptemys muhlenbergii and Clemmys guttata) should be considered as miniaturized. We employ geometric morphometric methods to quantify the patterns of shape change these potentially miniaturized species and their relatives undergo during ontogeny, and use molecular phylogenetic trees to reconstruct ancestral conditions and provide information on the polarity of shape changes. We find that differing changes in ontogenetic parameters relative to ancestral conditions accompany the evolution of small size in emydines: G. muhlenbergii changes the duration of ontogeny and rate of shape change, whereas C. guttata changes growth rate. The observed ontogenetic repatterning of these species is reminiscent of changes in ontogeny and life history often found in miniaturized taxa. However, we conclude that C. guttata and G. muhlenbergii are not truly miniaturized because they still produce typical adult shell morphologies, and larger emydines display comparable ontogenetic flexibility. Because no emydines carry juvenile shell features forward into adulthood, we speculate that few, if any turtles, will show paedomorphic shell traits without corresponding changes in defensive strategy because such shells may offer insufficient protection. © 2013 The Linnean Society of London     

Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher

Most Neotropical lowland forest taxa occur exclusively on one side of the Andes despite the availability of appropriate habitat on both sides. Almost all molecular phylogenies and phylogenetic analyses of species assemblages (i.e. area cladograms) have supported the hypothesis that Andean uplift during the Late Pliocene created a vicariant barrier affecting lowland lineages in the region. However, a few widespread plant and animal species occurring in lowland forests on both sides of the Andes challenge the generality of this hypothesis. To understand the role of the Andes in the history of such organisms, we reconstructed the phylogeographic history of a widespread Neotropical flycatcher (Mionectes oleagineus) in the context of the other four species in the genus. A molecular phylogeny based on nuclear and mitochondrial sequences unambiguously showed an early basal split between montane and lowland Mionectes. The phylogeographic reconstruction of lowland taxa revealed a complex history, with multiple cases in which geographically proximate populations do not represent sister lineages. Specifically, three populations of M. oleagineus west of the Andes do not comprise a monophyletic clade; instead, each represents an independent lineage with origins east of the Andes. Divergence time estimates suggest that at least two cross-Andean dispersal events post-date Andean uplift.     

A Holocene sequence of vegetation change at Lake Eteza, coastal KwaZulu-Natal, South Africa

Palynological and sedimentological data from a core extracted from Lake Eteza shed new light on the Holocene vegetation and climate history in KwaZulu-Natal and can be linked to regional and global climate change. A 2072 cm core with nineteen radiocarbon dates and chronological extrapolation to the bottom of the sequence suggests that sedimentation started ca. 10 200 cal yrs BP. Between ca. 10 200 and 6800 cal yrs BP pollen indicators point to a change from intermediately humid conditions to comparatively drier grassy environments. This is in good agreement with Sea Surface Temperature (SST) fluctuations from a core in the Mozambique Channel which influence precipitation in coastal KwaZulu-Natal, and the beginning of the Holocene Thermal Maximum ca. 10 500 cal yrs BP. The lower section of the core corresponds to gradually increasing Holocene sea levels along the coast and development of freshwater or estuarine conditions at Lake Eteza. The middle Holocene (ca. 6800-3600 cal yrs BP), when the sea level reached its highest stand and SST peak, indicate humid climatic conditions that favoured an increase of forest trees, e.g. Podocarpus, and undergrowth plants like Issoglossa. As a consequence of higher precipitation and increase of the water table, conditions were favourable for the spread of mangrove, swamp and possibly riverine forest. During the late Holocene after ca. 3600 cal yrs BP a decrease of Podocarpus and other trees as well as an increase of Chenopodiaceae/Amaranthaceae, grasses and Phoenix coincide with a return to lower sea levels and drier conditions. The decrease of all trees including Phoenix at ca. 700 cal yrs BP, accompanied by rapid sedimentation rates, possibly reflect forest clearing and upland erosion induced by activities of Iron Age settlers. A dry period at the globally recognized onset of the Little Ice Age might have contributed to these changes. Late Iron Age settlers have probably already introduced Zea mays, which was detected in the profile since ca. 210 BP. The appearance of neophytes like Pinus, Casuarina and pollen of Ambrosia-type in the youngest sediments indicates increased disturbance of European settlements and land use since ca. 100 cal yrs BP.     

The evolution of generalization? Parasitoid flies and the perils of inferring host range evolution from phylogenies

It is widely assumed that high resource specificity predisposes lineages toward greater likelihood of extinction and lower likelihood of diversification than more generalized lineages. This suggests that host range evolution in parasitic organisms should proceed from generalist to specialist, and specialist lineages should be found at the 'tips' of phylogenies. To test these hypotheses, parsimony and maximum likelihood methods were used to reconstruct the evolution of host range on a phylogeny of parasitoid flies in the family Tachinidae. In contrast to predictions, most reconstructions indicated that generalists were repeatedly derived from specialist lineages and tended to occupy terminal branches of the phylogeny. These results are critically examined with respect to hypotheses concerning the evolution of specialization, the inherent difficulties in inferring host ranges, our knowledge of tachinid-host associations, and the methodological problems associated with ancestral character state reconstruction. Both parsimony and likelihood reconstructions are shown to provide misleading results and it is argued that independent evidence, in addition to phylogenetic trees, is needed to inform models of the evolution of host range and the evolutionary consequences of specialization.