Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure

Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work.     

Fossil biogeography: a new model to infer dispersal,extinction and sampling from palaeontological data

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.     

Relaxed molecular clocks for dating historical plant dispersal events

Age estimation from molecular sequences has emerged as a powerful tool for inferring when a plant lineage arrived in a particular area. Knowing the tenure of lineages within a region is key to understanding the evolution of traits, the evolution of biotic interactions, and the evolution of floras. New analytical methods model change in substitution rates along individual branches of a phylogenetic tree by combining molecular data with time constraints, usually from fossils. These "relaxed clock" approaches can be applied to several gene regions that need not all have the same substitution rates, and they can also incorporate multiple simultaneous fossil calibrations. Since 1995, at least 100 plant biogeographic studies have used molecular-clock dating, and about a fifth has used relaxed clocks. Many of these report evidence of long-distance dispersal. Meta-analyses of studies from the same geographic region can identify directional biases because of prevailing wind or water currents and the relative position and size of landmasses.     

Extant primitively segmented spiders have recently diversified from an ancient lineage

Living fossils are lineages that have retained plesiomorphic traits through long time periods. It is expected that such lineages have both originated and diversified long ago. Such expectations have recently been challenged in some textbook examples of living fossils, notably in extant cycads and coelacanths. Using a phylogenetic approach, we tested the patterns of the origin and diversification of liphistiid spiders, a clade of spiders considered to be living fossils due to their retention of arachnid plesiomorphies and their exclusive grouping in Mesothelae, an ancient clade sister to all modern spiders. Facilitated by original sampling throughout their Asian range, we here provide the phylogenetic framework necessary for reconstructing liphistiid biogeographic history. All phylogenetic analyses support the monophyly of Liphistiidae and of eight genera. As the fossil evidence supports a Carboniferous Euramerican origin of Mesothelae, our dating analyses postulate a long eastward over-land dispersal towards the Asian origin of Liphistiidae during the Palaeogene (39–58 Ma). Contrary to expectations, diversification within extant liphistiid genera is relatively recent, in the Neogene and Late Palaeogene (4–24 Ma). While no over-water dispersal events are needed to explain their evolutionary history, the history of liphistiid spiders has the potential to play prominently in vicariant biogeographic studies.     

Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae

Annonaceae are a pantropically distributed family found predominantly in rainforests, so they are megathermal taxa, whereas Rhamnaceae are a cosmopolitan family that tend to be found in xeric regions and may be classified as mesothermal. Phylogenetic analyses of these families are presented based on rbcL and trnL-F plastid DNA sequences. Likelihood ratio tests revealed rate heterogeneity in both phylogenetic trees and they were therefore made ultrametric using non-parametric rate smoothing and penalized likelihood. Divergence times were then estimated using fossil calibration points. The historical biogeography of these families that are species rich in different biomes is discussed and compared with other published reconstructions. Rhamnaceae and most lineages within Annonaceae are too young to have had their distribution patterns influenced by break-up of previously connected Gondwanan landmasses. Contrasts in the degree of geographical structure between these two families may be explained by differences in age and dispersal capability. In both groups, long-distance dispersal appears to have played a more significant role in establishing modern patterns than had previously been assumed. Both families also contain examples of recent diversification of species-rich lineages. An understanding of the processes responsible for shaping the distribution patterns of these families has contributed to our understanding of the historical assembly of the biomes that they occupy.     

Tectonic blocks and molecular clocks

Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.     

Using directed phylogenetic networks to retrace species dispersal history

Methods designed for inferring phylogenetic trees have been widely applied to reconstruct biogeographic history. Because traditional phylogenetic methods used in biogeographic reconstruction are based on trees rather than networks, they follow the strict assumption in which dispersal among geographical units have occurred on the basis of single dispersal routes across regions and are, therefore, incapable of modelling multiple alternative dispersal scenarios. The goal of this study is to describe a new method that allows for retracing species dispersal by means of directed phylogenetic networks obtained using a horizontal gene transfer (HGT) detection method as well as to draw parallels between the processes of HGT and biogeographic reconstruction. In our case study, we reconstructed the biogeographic history of the postglacial dispersal of freshwater fishes in the Ontario province of Canada. This case study demonstrated the utility and robustness of the new method, indicating that the most important events were south-to-north dispersal patterns, as one would expect, with secondary faunal interchange among regions. Finally, we showed how our method can be used to explore additional questions regarding the commonalities in dispersal history patterns and phylogenetic similarities among species.     

Evolutionary islands in the Andes: persistence and isolation explain high endemism in Andean dry tropical forests

Aim The tropical Andes are a world biodiversity hotspot. With diverse biomes and dramatic, geologically recent mountain uplift, they offer a system to study the relative contributions of geological and biome history to species richness. There are preliminary indications that historical species assembly in the Andes has been influenced by physiographical heterogeneity and that distinct biomes have evolved in relative isolation despite physical proximity. Here we test this ‘Andean biotic separation hypothesis’ by focusing on the low‐elevation, seasonally dry tropical forest (SDTF) biome to determine whether patterns of plant diversification within the SDTF differ from those in mid‐ and high‐elevation biomes. Location Tropical Andes, South America. Methods Densely sampled time‐calibrated phylogenies for five legume genera (Amicia, Coursetia, Cyathostegia, Mimosa and Poissonia) containing species endemic to the Andean SDTF biome were used to investigate divergence times and levels of geographical structure. Geographical structure was measured using isolation‐by‐distance methods. Meta‐analysis of time‐calibrated phylogenies of Andean plant groups was used to compare the pattern and tempo of endemic species diversification between the major Andean biomes. Results Long‐term persistence of SDTF in the Andes is suggested by old stem ages (5–27 Ma) of endemic genera/clades within genera, and deep divergences coupled with strong geographical structure among and within species. Comparison of species diversification patterns among different biomes shows that the relatively old, geographically confined pattern of species diversification in SDTF contrasts with the high‐elevation grasslands that show rapid and recent radiations driven by ecological opportunities. Main conclusions The SDTF biome has a long history in the Andes. We suggest that the diverse SDTF flora has been assembled gradually over the past c. 19 Ma from lineages exhibiting strong phylogenetic niche conservatism. These patterns suggest that Andean SDTFs have formed stable and strongly isolated ‘islands’ despite the upheavals of Andean uplift. Indeed, the Andean SDTFs may represent some of the most isolated and evolutionarily persistent continental plant communities, similar in many respects to floras of remote oceanic islands.     

Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae

The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.     

Fossil‐based comparative analyses reveal ancient marine ancestry erased by extinction in ray‐finned fishes

The marine‐freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large‐scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant‐only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant‐only phylogenies.     

Biogeography and genome size evolution of the oldest extant vascular plant genus,Equisetum (Equisetaceae)

Background and AimsExtant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive phylogenetic analysis to date as a framework to evaluate their age, biogeography and genome size evolution.MethodsDNA sequences of four plastid loci were used to estimate divergence times and investigate the biogeographic history of all extant species of Equisetum. Flow cytometry was used to study genome size evolution against the framework of phylogenetic relationships in Equisetum.Key ResultsOn a well-supported phylogenetic tree including all extant Equisetum species, a molecular clock calibrated with multiple fossils places the node at which the outgroup and Equisetum diverged at 343 Mya (Early Carboniferous), with the first major split among extant species occurring 170 Mya (Middle Jurassic). These dates are older than those reported in some other recent molecular clock studies but are largely in agreement with a timeline established by fossil appearance in the geological record. Representatives of evergreen subgenus Hippochaete have much larger genome sizes than those of deciduous subgenus Equisetum, despite their shared conserved chromosome number. Subgenus Paramochaete has an intermediate genome size and maintains the same number of chromosomes.ConclusionsThe first divergences among extant members of the genus coincided with the break-up of Pangaea and the resulting more humid, warmer climate. Subsequent tectonic activity most likely involved vicariance events that led to species divergences combined with some more recent, long-distance dispersal events. We hypothesize that differences in genome size between subgenera may be related to the number of sperm flagellae.     

Testing alternative vicariance scenarios in Western Mediterranean discoglossid frogs

Dated molecular phylogenies are often used to interpret evolutionary history with respect to paleogeographic events. Where more than one interpretation is possible, it is desirable but difficult to assess the alternatives in an objective manner. The present work demonstrates a formalized method for testing molecular clock calibrations and biogeographic scenarios based on them. We assessed the plausibility of several previously published biogeographic hypotheses, using the frog genera Alytes, Discoglossus, and Bombina as model groups. Our data set comprised ca. 900bp of partial mitochondrial 16S and 12S rRNA gene sequences (both genes evolved in a clock-like manner across genera) from nearly all the species and subspecies in the three genera. We tested several calibrations of a molecular clock, which resulted in competing temporal settings for the evolution of taxa. Although only one scenario was in complete accordance with paleogeographic data, statistical testing did not reject the alternatives. Limitations encountered with the present approach may be overcome by more comprehensive analyses in future.     

Bayesian analysis of combined chloroplast loci, using multiple calibrations, supports the recent arrival of Melastomataceae in Africa and Madagascar

A new biogeographic scenario for Melastomataceae (Morley and Dick, American Journal of Botany 90(11) pp. 1638-1645, 2003) accepts an ndhF-based phylogeny for the family by Renner et al. (American Journal of Botany 88(7): 1290-1300, 2001), but rejects those authors' divergence time estimates. Morley and Dick concluded that Gondwanan vicariance, rather than the more recent long dispersal proposed by Renner et al. explains the presence of the family in Africa and Madagascar. To assess the strength of this conclusion, a Bayesian analysis was conducted on three times the amount of sequence data used before (ndhF, rbcL, rpl16; 3100 base pairs [bp], excluding all gaps). The Bayesian approach to divergence time estimation does not rely on a strict molecular clock and employs multiple simultaneous minimal or maximal bounds on node ages. Reliance on northern mid-latitude fossils of Melastomataceae for calibrations was avoided or reduced by using alternative fossil and tectonic calibrations, including all those suggested by Morley and Dick. Results reaffirm the relatively recent spread of melastome lineages among the southern continents and refute the breakup of Gondwana as a plausible explanation for the presence of Dissochaeteae/Sonerileae in Madagascar and Africa and the presence of Melastomeae in Africa and Southeast Asia. Melastomeae appear to have reached Africa around 17-15 million years (my) ago, while Dissochaeteae and Sonerileae apparently reached Madagascar at 17-15 and 20-18 my ago. I also explored the effects of constraining Melastomeae to minimally 76 my old (to have reached Africa by island hopping as postulated by Morley and Dick). This resulted in an estimate for their arrival in Africa of 35 my ago and for Dissochaeteae and Sonerileae in Madagascar of 28 and 33 my ago, still implying long-distance dispersal. The Bayesian 95% credibility ranges around these dates, however, are large. Regardless of the increasing sophistication of molecular estimates of divergence time, Gondwanan scenarios will remain untestable as long as biases in the fossil record can justifiably be invoked to explain away the absence of fossils.     

Unravelling the evolutionary origins of biogeographic assemblages

Aim

Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping present‐day diversity patterns and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of present‐day biogeographic assemblages and highlight their conservation value.

Location

Southern Africa.

Methods

We evaluate the evolutionary turnover separating species clusters in space at different time slices to determine the phylogenetic depth at which the signal for their present‐day structure emerges. We suggest present‐day assemblages with distinct evolutionary histories might represent important units for conservation. We apply our method to the vegetation of southern Africa using a dated phylogeny of the woody flora of the region and explore how the evolutionary history of vegetation types compares to common conservation currencies, including species richness, endemism and threat.

Results

We show the differentiation of most present‐day vegetation types can be traced back to evolutionary splits in the Miocene. The woody flora of the Fynbos is the most evolutionarily distinct, and thus has deeper evolutionary roots, whereas the Savanna and Miombo Woodland show close phylogenetic affinities and likely represent a more recent separation. However, evolutionarily distinct phyloregions do not necessarily capture the most unique phylogenetic diversity, nor are they the most species‐rich or threatened.

Main conclusions

Our approach complements analyses of the fossil record and serves as a link to the history of diversification, migration and extinction of lineages within biogeographic assemblages that is separate from patterns of species richness and endemism. Our analysis reveals how phyloregions capture conservation value not represented by traditional biodiversity metrics.

     

Age of cichlids: new dates for ancient lake fish radiations

Timing divergence events allow us to infer the conditions under which biodiversity has evolved and gain important insights into the mechanisms driving evolution. Cichlid fishes are a model system for studying speciation and adaptive radiation, yet, we have lacked reliable timescales for their evolution. Phylogenetic reconstructions are consistent with cichlid origins prior to Gondwanan landmass fragmentation 121-165 MYA, considerably earlier than the first known fossil cichlids (Eocene). We examined the timing of cichlid evolution using a relaxed molecular clock calibrated with geological estimates for the ages of 1) Gondwanan fragmentation and 2) cichlid fossils. Timescales of cichlid evolution derived from fossil-dated phylogenies of other bony fishes most closely matched those suggested by Gondwanan breakup calibrations, suggesting the Eocene origins and marine dispersal implied by the cichlid fossil record may be due to its incompleteness. Using Gondwanan calibrations, we found accumulation of genetic diversity within the radiating lineages of the African Lakes Malawi, Victoria and Barombi Mbo, and Palaeolake Makgadikgadi began around or after the time of lake basin formation. These calibrations also suggest Lake Tanganyika was colonized independently by the major radiating cichlid tribes that then began to accumulate genetic diversity thereafter. These results contrast with the widely accepted theory that diversification into major lineages took place within the Tanganyika basin. Together, this evidence suggests that ancient lake habitats have played a key role in generating and maintaining diversity within radiating lineages and also that lakes may have captured preexisting cichlid diversity from multiple sources from which adaptive radiations have evolved.     

Trans-oceanic dispersal and evolution of early composites (Asteraceae)

How did Asteraceae (the daisy family) expand from its area of origin and become so widespread? This question has challenged generations of evolutionary botanists. Molecular phylogenetic and biogeographic analyses indicate a South American origin of Asteraceae, a view supported by the recent discovery of the earliest fossils of the family in Middle Eocene (ca. 50 Ma) deposits in southern South America. The early-branching lineages in the phylogenetic tree of Asteraceae are South American and African, suggesting that the earliest successful colonization of areas outside South America may have involved long-distance dispersal to Africa. However, one particularly challenging unanswered question is how early members of Asteraceae reached Africa at a time when the Atlantic Ocean constituted a barrier between the two continents. Morphological, phylogenetic, geographic, paleogeographic, and paleontologic data have been combined to propose scenarios on possible geographical and dispersal routes and vectors of dispersion of early-branching lineages of Asteraceae from South America to Africa. Of the different scenarios proposed here, two concern alternative geographical routes: (1) via the Rio Grande Rise-Walvis Ridge axis in the South Atlantic; or (2) via Antarctica, possibly including the Subantarctic islands. Three scenarios consider different dispersal routes: (1) stepping-stones; (2) single-step; and (3) sweepstakes. Finally, three vectors of dispersion are considered: (1) birds; (2) wind; and (3) floating islands. Evaluation of these scenarios suggests that early-branching lineages of Asteraceae probably dispersed from South America to Africa along an island chain formed by the Rio Grande Rise and the Walvis Ridge, transported by birds, possibly combined with rafting and/or sweepstakes. Morphological changes typically associated with evolution on islands characterize many African carduoid descendants, providing indirect evidence for step-wise dispersal along the island chain.     

Multilocus phylogenetic and geospatial analyses illuminate diversification patterns and the biogeographic history of Malagasy endemic plated lizards (Gerrhosauridae: Zonosaurinae)

Although numerous studies have attempted to find single unifying mechanisms for generating Madagascar's unique flora and fauna, little consensus has been reached regarding the relative importance of climatic, geologic and ecological processes as catalysts of diversification of the region's unique biota. Rather, recent work has shown that both biological and physical drivers of diversification are best analysed in a case‐by‐case setting with attention focused on the ecological and life‐history requirements of the specific phylogenetic lineage under investigation. Here, we utilize a comprehensive analytical approach to examine evolutionary drivers and elucidate the biogeographic history of Malagasy plated lizards (Zonosaurinae). Data from three genes are combined with fossil information to construct time‐calibrated species trees for zonosaurines and their African relatives, which are used to test alternative diversification hypotheses. Methods are utilized for explicitly incorporating phylogenetic uncertainty into downstream analyses. Species distribution models are created for 14 of 19 currently recognized species, which are then used to estimate spatial patterns of species richness and endemicity. Spatially explicit analyses are employed to correlate patterns of diversity with both topographic heterogeneity and climatic stability through geologic time. We then use inferred geographic ranges to estimate the biogeographic history of zonosaurines within each of Madagascar's major biomes. Results suggest constant Neogene and Quaternary speciation with divergence from the African most recent common ancestor ~30 million years ago when oceanic currents and African rivers facilitated dispersal. Spatial patterns of diversity appear concentrated along coastal regions of northern and southern Madagascar. We find no relationship between either topographic heterogeneity or climatic stability and patterns of diversity. Ancestral state reconstructions suggest that western dry forests were important centres of origin with recent invasion into spiny and rain forest. These data highlight the power of combining multilocus phylogenetic and spatially explicit analyses for testing alternative diversification hypotheses within Madagascar's unique biota and more generally, particularly as applied to phylogenetically and biologically constrained systems.     

Phylogeography of Poorly Dispersing Net-Winged Beetles: A Role of Drifting India in the Origin of Afrotropical and Oriental Fauna

Ancient dispersal history may be obscured by subsequent dispersal events. Therefore, we intend to investigate the biogeography of metriorrhynchine net-winged beetles, a group characterized by limited dispersal propensity. We used DNA data to construct phylogenies and the BayesTraits and RASP programs to identify putative ancestral areas. Further, we inferred ultrametric trees to estimate the ages of selected nodes. The time frame is inferred from tectonic calibrations and the general mutation rate of the mitochondrial genes. Metriorrhynchini consists of two lineages with Afro/Oriental and Australian distributions. The basal lineages originated in Eastern Gondwana after the split of Australia, India and Madagascar; the Afrotropical and Madagascar Metriorrhynchini separated from the Oriental clades 65 and 62 mya. Several already diversified lineages colonized continental Asia 55–35 mya. A few genera of the Australian clade dispersed to the Oriental region 5–15 mya and reached Eastern India and Southern China. Only Xylobanus crossed the Makassar Strait to Sulawesi and does not occur further to the east. The current distribution of Metriorrhynchini is a result of drifting on continental fragments and over-sea dispersal events limited to a few hundreds of kilometers. We conclude that: (1) Afrotropical and Madagascar lineages originated independently from dispersal events during India''s drift to the north and the Mozambique Channel completely isolates the respective faunas since then; (2) Oriental fauna is a recently established mixture of the Indian and Australian lineages, with predominance of the older Indian clades; (3) The fauna of islands located north of Australia colonized Sulawesi after collision with the Sundaland margin and the species rich Australian lineages did not reach Western Wallacea or the Philippines. Our results suggest an impact of subtle differences in biological characteristics on biogeographic history of individual lineages, when mostly lowland and flower-visiting lineages were able to disperse across sea channels.     

Phylogeny of the tribe Indigofereae (Leguminosae-Papilionoideae): Geographically structured more in succulent-rich and temperate settings than in grass-rich environments

This analysis goes beyond many phylogenies in exploring how phylogenetic structure imposed by morphology, ecology, and geography reveals useful evolutionary data. A comprehensive range of such diversity is evaluated within tribe Indigofereae and outgroups from sister tribes. A combined data set of 321 taxa (over one-third of the tribe) by 80 morphological characters, 833 aligned nuclear ribosomal ITS/5.8S sites, and an indel data set of 33 characters was subjected to parsimony analysis. Notable results include the Madagascan dry forest Disynstemon resolved as sister to tribe Indigofereae, and all species of the large genus Indigofera comprise just four main clades, each diagnosable by morphological synapomorphies and ecological and geographical predilections. These results suggest niche conservation (ecology) and dispersal limitation (geography) are important processes rendering signature shapes to the Indigofereae phylogeny in different biomes. Clades confined to temperate and succulent-rich biomes are more dispersal limited and have more geographical phylogenetic structure than those inhabiting tropical grass-rich vegetation. The African arid corridor, particularly the Namib center of endemism, harbors many of the oldest Indigofera lineages. A rates analysis of nucleotide substitutions confirms that the ages of the oldest crown clades are mostly younger than 16 Ma, implicating dispersal in explaining the worldwide distribution of the tribe.