Biogeography is the discipline of biology that studies the present and past distribution patterns of biological diversity and their underlying environmental and historical causes. For most of its ...history, biogeography has been divided into proponents of vicariance explanations, who defend that distribution patterns can mainly be explained by geological, tectonic-isolating events; and dispersalists, who argue that current distribution patterns are largely the result of recent migration events. This paper provides an overview of the evolution of the discipline from methods focused on finding general patterns of distribution (cladistic biogeography), to those that integrate biogeographic processes (event-based biogeography), to modern probabilistic approaches (parametric biogeography). The latter allows incorporating into biogeographic inference estimates of the divergence time between lineages (usually based on DNA sequences) and external sources of evidence, such as information on past climate and geography, the organism fossil record, or its ecological tolerance. This has revolutionized the discipline, allowing it to escape the dispersal versus vicariance dilemma and to address a wider range of evolutionary questions, including the role of ecological and historical factors in the construction of biomes or the existence of contrasting patterns of range evolution in animals and plants.
Aim The geological evolution of the Mediterranean region is largely the result of the Tertiary collision of the African and Eurasian Plates, but also a mosaic of migrating island arcs, fragmenting ...tectonic belts, and extending back-arc basins. Such complex paleogeography has resulted in a 'reticulate' biogeographical history, in which Mediterranean biotas repeatedly fragmented and merged as dispersal barriers appeared and disappeared through time. In this study, dispersal-vicariance analysis (DIVA) is used to assess the relative role played by dispersal and vicariance in shaping distribution patterns in the beetle subfamily Pachydeminae Reitter, 1902 (Scarabaeoidea), an example of east-west Mediterranean disjunction. Location The Mediterranean region, including North Africa, the western Mediterranean, Balkans-Anatolia, Middle East, Caucasus, the Iranian Plateau, and Central Asia. Methods A phylogenetic hypothesis of the Palearctic genera of Pachydeminae in conjunction with distributional data was analysed using DIVA. This method reconstructs the ancestral distribution in a given phylogeny based on the vicariance model, while allowing dispersal and extinction to occur. Unlike other methods, DIVA does not enforce area relationships to conform to a hierarchical 'area cladogram', so it can be used to reconstruct 'reticulate' biogeographical scenarios. Results Optimal reconstructions, requiring 23 dispersal events, suggest that the ancestor of Pachydeminae was originally present in the south-east Mediterranean region. Basal splitting within the subfamily was caused by vicariance events related to the late Tertiary collision of the African microplates Apulia and Arabia with Eurasia, and the resultant arise of successive dispersal barriers (e.g. the Red Sea, the Zagros Mountains). Subsequent diversification in Pachydeminae involved multiple speciation events within the Middle East and Iran-Afghanistan regions, which gave rise to the least speciose genera of Pachydeminae (e.g. Otoclinius Brenske, 1896). Finally, the presence of Pachydeminae in the western Mediterranean region seems to be the result of a recent dispersal event. The ancestor of the Iberian genera Ceramida Baraud, 1987 and Elaphocera Gené, 1836 probably dispersed from the Middle East to the Iberian Peninsula across North Africa and the Gibraltar Strait during the 'Messinian salinity crisis' at the end of the Miocene. Main conclusions Although the basal diversification of Pachydeminae around the Mediterranean appears to be related to vicariance events linked to the geological formation of the Mediterranean Basin, dispersal has also played a very important role. Nearly 38% of the speciation events in the phylogeny resulted from dispersal to a new area followed by allopatric speciation between lineages. Relationships between western and eastern Mediterranean disjuncts are usually explained by dispersal through Central Europe. The biogeographical history of the Pachydeminae corroborates other biogeographical studies that consider North Africa to be an alternative dispersal route by which Mediterranean taxa could have achieved circum-Mediterranean distributions.
Phylogenetic Methods in Biogeography Ronquist, Fredrik; Sanmartín, Isabel
Annual review of ecology, evolution, and systematics,
12/2011, Letnik:
42, Številka:
1
Journal Article
Recenzirano
Phylogenetic approaches to biogeography are rapidly becoming more sophisticated. Four types of models are being explored in the literature: (
a
) diffusion models, (
b
) island models, (
c
) ...hierarchical vicariance models (HVMs), and (
d
) reticulate models. Diffusion models are used primarily for phylogeographic inference but can also offer insights into geographic discontinuities of significance on longer time scales. For the island models, statistical approaches are now well developed and typically offer more detailed insight than parsimony analysis. In contrast, parsimony may still be the best option for HVM analysis, because existing statistical approaches do not yet accommodate dispersal. The proposed probabilistic models of reticulate scenarios remain poorly understood, even though they may currently do the best job of integrating diversification processes into biogeographic analysis. Statistical approaches are gaining in popularity across the field, in part because of the flexibility of stochastic modeling. This allows investigators to address important related processes, such as ecological interactions and climate change, in biogeographic inference.
The Neotropical region (tropical America) is the most species rich region on Earth. Several causes have been proposed to explain this extraordinary biodiversity, which may be very roughly classified ...into two major categories: 'biotic' (e.g. soil adaptations; biotic interactions with pollinators, dispersers and herbivores; niche conservatism; dispersal ability) and 'abiotic' (e.g. time; rainfall, temperature and area; mountain uplift; hydrological changes). In this paper we review the evidence for each of these postulated causes of diversification and provide general directions towards further testing. We highlight the need of more well-sampled and dated phylogenies and urge increased inter-disciplinary collaboration.
Modelling the tempo and mode of lineage dispersal Hackel, Jan; Sanmartín, Isabel
Trends in ecology & evolution (Amsterdam),
December 2021, 2021-12-00, 20211201, Letnik:
36, Številka:
12
Journal Article
Recenzirano
Lineage dispersal is a basic macroevolutionary process shaping the distribution of biodiversity. Probabilistic approaches in biogeography, epidemiology, and macroecology often model dispersal as a ...background process to explain extant or infer past distributions. We propose framing questions around the mode, timing, rate, and direction of lineage dispersal itself, from a lineage- or geography-centric perspective. We review available methods for modelling lineage dispersal. Likelihood- and simulation-based approaches to modelling dispersal have made progress in accounting for the variation of lineage dispersal over space, time, and branches of a phylogeny and its interaction with diversification. Methodological improvements, guided by a focus on model adequacy, will lead to more realistic models that can answer fundamental questions about the tempo and mode of lineage dispersal.
Lineage dispersal is central to macroevolution but often modelled only as a background process.Focusing on the mode, direction, timing, and rate of lineage dispersal, from either a lineage or geographic perspective, provides a framework for inferences about the process itself.Probabilistic models increasingly capture the variation of lineage dispersal over space, time, and branches and its interaction with diversification.Methodological advances will help answer fundamental biological questions about the role of lineage dispersal through time, space, and across the tree of life.
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•Outline of the modular structure of phylogenetic models.•Individual models can be combined into a single supermodel.•Pedagogical overview of the mathematical structure of ...models.•Graphical display of model structure.
The field of phylogenetics has burgeoned into a great diversity of statistical models, providing researchers with a vast amount of analytical tools for investigating the evolutionary theory. This abundance of theoretical work has the merit that many different aspects of evolution can be investigated using various types of data. However, empiricists may sometimes struggle to find the right model for their needs amid such variety. In particular, some computer programs gather the theory of many different models, published in hundreds of different papers, within the same operational framework. This makes it particularly difficult for users to obtain comprehensive information about the assumptions and structure of various models. Yet, a large part of phylogenetic models are structured in individual modules that can be linked together in the same conceptual framework, akin to some sort of phylogenetic supermodel. In this paper, we propose to browse through the network of phylogenetic models, emphasizing their modular structure, with the purpose to outline the commonalities and differences of individual models. Focusing on probabilistic models, we describe how to go from the model assumptions to the corresponding probability distributions as pedagogically as possible. To achieve this task, we resort heavily on graph theory to represent the probabilistic relationships among parameters and data, and present the models in their most elementary form (i.e. including parameters that are generally marginalized out), which simplifies the mathematics considerably. We concentrate on models designed for species trees, but evoke the link with other types of trees (e.g. gene trees).
Phylogenese studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal-extinction-cladogenesis (DEC) model, especially ...between DEC and DEC+J, a variant that emphasizes "jump dispersal," or founder-event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founderevent speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time-dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non-jump events is assigned a free parameter, j, that when maximized precludes the possibility of non-jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the "true" model of range evolution, which surely must include time-dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time-dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state-dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC-based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.
The European steppes and their biota have been hypothesized to be either young remnants of the Pleistocene steppe belt or, alternatively, to represent relicts of long-term persisting populations; ...both scenarios directly bear on nature conservation priorities. Here, we evaluate the conservation value of threatened disjunct steppic grassland habitats in Europe in the context of the Eurasian steppe biome. We use genomic data and ecological niche modelling to assess pre-defined, biome-specific criteria for three plant and three arthropod species. We show that the evolutionary history of Eurasian steppe biota is strikingly congruent across species. The biota of European steppe outposts were long-term isolated from the Asian steppes, and European steppes emerged as disproportionally conservation relevant, harbouring regionally endemic genetic lineages, large genetic diversity, and a mosaic of stable refugia. We emphasize that conserving what is left of Europe's steppes is crucial for conserving the biological diversity of the entire Eurasian steppe biome.
Recent phylogenetic studies have revealed the major role played by the uplift of the Andes in the extraordinary diversification of the Neotropical flora. These studies, however, have typically ...considered the Andean uplift as a single, time-limited event fostering the evolution of highland elements. This contrasts with geological reconstructions indicating that the uplift occurred in discrete periods from west to east and that it affected different regions at different times. We introduce an approach for integrating Andean tectonics with biogeographic reconstructions of Neotropical plants, using the coffee family (Rubiaceae) as a model group. The distribution of this family spans highland and montane habitats as well as tropical lowlands of Central and South America, thus offering a unique opportunity to study the influence of the Andean uplift on the entire Neotropical flora. Our results suggest that the Rubiaceae originated in the Paleotropics and used the boreotropical connection to reach South America. The biogeographic patterns found corroborate the existence of a long-lasting dispersal barrier between the Northern and Central Andes, the "Western Andean Portal." The uplift of the Eastern Cordillera ended this barrier, allowing dispersal of boreotropical lineages to the South, but gave rise to a huge wetland system ("Lake Pebas") in western Amazonia that prevented in situ speciation and floristic dispersal between the Andes and Amazonia for at least 6 million years. Here, we provide evidence of these events in plants.
Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We ...test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study.
Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multi-species-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times.
Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern.
We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.
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