Phylogeography of the North American red fox: vicariance in Pleistocene forest refugia

Fossil, archaeological, and morphometric data suggest that indigenous red foxes in North America were derived from vicariance in two disjunct refugia during the last glaciation: one in Beringia and one in the contiguous USA. To test this hypothesis, we conducted a phylogeographical analysis of the North American red fox within its presettlement range. We sequenced portions of the mitochondrial cytochrome b (354 bp) gene and D-loop (342 bp) from 220 historical red fox specimens. Phylogenetic analysis of the cytochrome b gene produced two clades that diverged c . 400 000 years before present ( bp ): a Holarctic and a Nearctic clade. D-loop analyses of the Nearctic clade indicated three distinct subclades (≥ 99% Bayesian posterior probability); two that were more recently derived (rho estimate c . 20 000 bp ) and were restricted to the southwestern mountains and the eastern portion of North America, and one that was older (rho estimate c . 45 000 bp ) and more widespread in North America. Populations that migrated north from the southern refugium following deglaciation were derived from the colonization of North America during or prior to the Illinoian glaciation (300 000–130 000 bp ), whereas populations that migrated south from the northern refugium represent a more recent colonization event during the Wisconsin glaciation (100 000–10 000 bp ). Our findings indicate that Nearctic clade red foxes are phylogenetically distinct from their Holarctic counterparts, and reflect long-term isolation in two disjunct forest refugia during the Pleistocene. The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct.     

Scales of climatic variability and time averaging in Pleistocene biotas: implications for ecology and evolution

Biotic responses to Pleistocene climatic fluctuations have traditionally been analyzed in the context of glacial-interglacial cycles on the scale of 10000-100 000 years. However, emerging evidence indicates that short-term, high-amplitude, climatic 'flickers', close to the limits of the resolving power of the fossil record, occurred within the glacial and interglacial substages. Because species shift geographically in response to the climate flickers, community structures are fluid, with changes absorbed ecologically and not mediated macroevolutionarily. The rapidity of these shifts may also explain anomalous fossil assemblages.     

The role of remnant forest trees in tropical secondary succession

This paper emphasizes the contribution of remnant trees to the establishment of woody species during succession on abandoned fields and pastures in the Mexican rain forest area, Los Tuxtlas, Veracruz. Remnant trees, original large forest trees left in the clearings by traditional farmers will become natural perching sites for both passing and resident birds. Frugivorous birds drop or regurgitate seeds and fruits which fall under the canopies of remnant trees during their stay, thus contributing to an accumulation of species, which make these remnant trees into ‘regeneration nuclei’. The species transported into these sites belong chiefly to older stages of successional development and reach these otherwise isolated areas, counteracting the depauperization of tropical land, brought about by both intensive and extensive clearing. In a study of seven remnant trees, 29 woody species and two climbers were found, 86% of which are bird dispersed. The total number of species per tree varied from 6 to 15 and was higher under remnant trees with fruits attractive to birds. Floristic variations of the understorey as detected by detrended correspondence analysis was correlated with the relative amount of shade-tolerant primary and late secondary trees versus light dependent pioneers and early successional trees.     

The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas

Biodiversity is unevenly distributed on Earth and hotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history (i.e. tens of millions of years). Understanding the underlying processes that have driven the accumulation of species in some areas and not in others may help guide prioritization in conservation and may facilitate forecasts on ecosystem services under future climate conditions. Consequently, the study of the origin and evolution of biodiversity in mountain systems has motivated growing scientific interest. Despite an increasing number of studies, the origin and evolution of diversity hotspots associated with the Qinghai‐Tibetan Plateau (QTP) remains poorly understood. We review literature related to the diversification of organisms linked to the uplift of the QTP. To promote hypothesis‐based research, we provide a geological and palaeoclimatic scenario for the region of the QTP and argue that further studies would benefit from providing a complete set of complementary analyses (molecular dating, biogeographic, and diversification rates analyses) to test for a link between organismic diversification and past geological and climatic changes in this region. In general, we found that the contribution of biological interchange between the QTP and other hotspots of biodiversity has not been sufficiently studied to date. Finally, we suggest that the biological consequences of the uplift of the QTP would be best understood using a meta‐analysis approach, encompassing studies on a variety of organisms (plants and animals) from diverse habitats (forests, meadows, rivers), and thermal belts (montane, subalpine, alpine, nival). Since the species diversity in the QTP region is better documented for some organismic groups than for others, we suggest that baseline taxonomic work should be promoted.     

Molecular evidence for Pleistocene refugia at the eastern edge of the Tibetan Plateau

The role of the Quaternary ice ages in forming the contemporary genetic structure of populations has been well studied in a number of global regions. However, due to the different nature of glaciations and complex topography, their role in shaping eastern Eurasian genetic diversity, particular in areas surrounding the Tibetan Plateau have remained largely unstudied. We aimed to address this question by examining the genetic structure of an alpine forest-associated taxon, the blood pheasant (Ithaginis cruentus) to infer its phylogeographic history. We detected three phylogenetic lineages and four current population groups. By comparing molecular and palaeovegetation data, we found that major glaciations during the Pleistocene have had a major impact upon the current genetic diversity of this species. Coalescent simulations indicate that the populations retreated to different refugia during some glacial periods in the Pleistocene, but persisted through the last glacial maximum (LGM). The most significant recent population expansion was found to have occurred before the LGM, during which palaeoclimatic data indicate that the climate was both warmer and wetter than today. In contrast, during the LGM populations may have adopted an altitudinal shift strategy in order to track changes in alpine glaciers, exemplifying a general response for montane species in the region where alpine glaciations were not large enough to cause qualitative changes in vegetation. Although analysis based on a plumage related gene showed that divergent selection may have contributed to current patterns of intra-specific diversity, demographic isolation is inferred to have played a more dominant role.     

Evidence of late Pleistocene fires and eucalypt forest from a North Queensland humid tropical rainforest site

Charcoal fragments, some identified as Eucalyptus, with radiocarbon dates spanning the period 27 000–12 000 years bp , were found in a soil profile under moist tropical rainforest in north-eastern Australia. The charcoal indicates that sclerophyll forest occupied a central part of the Windsor Tableland rainforest massif during the late Pleistocene. The widespread presence of identifiable and dateable charcoal under rainforest in north Queensland provides an opportunity to examine the patterns and ecological implications of fluctuations in rainforest distribution in recent history.     

Tree species diversity in temperate and tropical forest gaps: The role of lottery recruitment

How canopy gaps promote tree species coexistence in temperate and tropical forests is reviewed. Given that evidence for traditional resource-based niche partitioning of canopy gaps is weak, lottery recruitment, whereby colonization of vacant living space is random with respect to species identity, may be key to maintaining diversity. Gap formation events are not highly predictable and species’ propagules tend to be patchily distributed. For these reasons the predictability of gap-phase recruitment is low and lottery principles apply. Recruitment limitation from discontinuities in species’ propagule supplies in space and time may permit lottery recruitment in temperate and tropical forests. However, the relative importance of recruitment limitation in species-rich versus species-poor communities is unclear. Although lottery models with purely random recruitment in vacant sites can be applied, relatively complex models appear to better capture the essential features of forest community dynamics. For example, models with recruitment probabilities weighted by species abundance can produce the non-random trajectories often observed in communities. Models with local competitive displacement by individuals of dominant species can also produce non-random trajectories. Models with spatial structure, localized competition, and dispersal limitations may provide further insight into the effects of biotic interactions and recruitment limitation on forest dynamics.     

Environment,preferred habitats and potential refugia for Pleistocene Homo in Southeast Asia

Multiple lines of evidence suggest that Southeast Asia was dominated by a mix of savannah, open woodlands, and evergreen forests throughout much of the Pleistocene. These conditions are ideal for early hominin subsistence; however, they would have been rare for much of the rest of Asia during glacial periods. We explore the possibility that Southeast Asia would have served as a refugium for hominins during these periods. In particular, we draw parallels with the population source and sink model proposed for northern Europe (Dennell et al., 2010), with Southeast Asia acting as a population source and northern China acting as a population sink.     

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa

Understanding the history of forests and their species'' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation—coastal or swamp vs terra firme—in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.     

Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob)

Mitochondrial DNA control region sequences and seven microsatellites were used to estimate the genetic structuring, evolutionary history and historic migration patterns of the kob antelope (Kobus kob). Ten populations were analysed, representing the three recognized K. kob subspecies: K. k. kob in west Africa, K. k. thomasi in Uganda and K. k. leucotis in Sudan and Ethiopia. Despite being classified as K. k. thomasi and being phenotypically identical to the kob in Queen Elizabeth National Park (NP), the Murchison Falls population in Uganda showed high genetic similarity with the phenotypically distinct K. k. leucotis populations in Sudan and Ethiopia. This was regardless of marker type. Pairwise comparisons and genetic distances between populations grouped Murchison with K. k. leucotis, as did the Bayesian analysis, which failed to find any genetic structuring within the group. We propose that the divergent phenotype and life-history adaptations of K. k. leucotis reflect the isolation of kob populations in refugia in west and east Africa during the Pleistocene. Subsequent dispersal has led to secondary contact and hybridization in northern Uganda between lineages, which was supported by high levels of genetic diversity in Murchison. The reduced variability observed in Queen Elizabeth NP reflects a small founder population from west Africa and in part the decimation of Uganda's wildlife during the country's political turmoil in the 1970s. Due to similarities in phenotype and ecology, and the joint evolutionary history of their mtDNA sequences, the taxonomic status of K. k. kob and K. k. thomasi as separate subspecies is called into question.     

The significance of island biotas

Island biotas have played a significant part in evolutionary biology, because they are so often starkly different from continental biotas (even though it took Darwin some time to realize this; his visit to the Galapagos Islands was not the converting experience often claimed for it). In recent years, most interest has concentrated on species diversity on islands, but differentiation of endemics is probably worth more attention. Key factors in the evolution of island forms include the complementary processes of Mayr's 'genetic revolution' (a genetic bottleneck, particularly when a previously empty area is colonized; and adaptation in isolation), the opportunistic (not perfecting) nature of natural selection, and the ecological history of island colonists.     

The West Indies as a laboratory of biogeography and evolution

Islands have long provided material and inspiration for the study of evolution and ecology. The West Indies are complex historically and geographically, providing a rich backdrop for the analysis of colonization, diversification and extinction of species. They are sufficiently isolated to sustain endemic forms and close enough to sources of colonists to develop a dynamic interaction with surrounding continental regions. The Greater Antilles comprise old fragments of continental crust, some very large; the Lesser Antilles are a more recent volcanic island arc, and the low-lying Bahama Islands are scattered on a shallow oceanic platform. Dating of island lineages using molecular methods indicates over-water dispersal of most inhabitants of the West Indies, although direct connections with what is now southern Mexico in the Early Tertiary, and subsequent land bridges or stepping stone islands linking to Central and South America might also have facilitated colonization. Species-area relationships within the West Indies suggest a strong role for endemic radiations and extinction in shaping patterns of diversity. Diversification is promoted by opportunities for allopatric divergence between islands, or within the large islands of the Greater Antilles, with a classic example provided by the Anolis lizards. The timing of colonization events using molecular clocks permits analysis of colonization-extinction dynamics by means of species accumulation curves. These indicate low rates of colonization and extinction for reptiles and amphibians in the Greater Antilles, with estimated average persistence times of lineages in the West Indies exceeding 30Myr. Even though individual island populations of birds might persist an average of 2Myr on larger islands in the Lesser Antilles, recolonization from within the archipelago appears to maintain avian lineages within the island chain indefinitely. Birds of the Lesser Antilles also provide evidence of a mass extinction event within the past million years, emphasizing the time-heterogeneity of historical processes. Geographical dynamics are matched by ecological changes in the distribution of species within islands over time resulting from adaptive radiation and shifts in habitat, often following repeatable patterns. Although extinction is relatively infrequent under natural conditions, changes in island environments as a result of human activities have exterminated many populations and others--especially old, endemic species--remain vulnerable. Conservation efforts are strengthened by recognition of aesthetic, cultural and scientific values of the unique flora and fauna of the West Indies.     

Butterfly biogeography and endemism on tropical Pacific islands

Butterfly distributions on 26 tropical Pacific archipelagos were analysed to examine the effects of geography on diversity and endemism. The total butterfly fauna for each archipelago was divided into continental (found also on continental areas), Pacific (found within more than one archipelago but not outside of the study area), and endemic species (restricted to a single archipelago). Numbers and proportions of each species were related to eight geographic variables by stepwise multiple linear regression analysis. Total area of an archipelago and distance from other land masses were important predictors of the number of species within an archipelago. Proportions of butterfly species in each category were related differently to the geographic variables, with endemism being promoted by the number of large islands within an archipelago. Relative to birds, butterflies have been less successful in colonizing remote archipelagos and have much lower levels of endemism. Even if colonization is successful, butterfly speciation may be constrained by the mechanics of coevolution with available host plants.     

The ediacaran biotas in space and time

The "Ediacaran organisms," which preceded and overlapped the Cambrian radiation of metazoans, include many fossils whose systematic positions remain contentious after over fifty years of study. It might seem that nothing particularly useful can be learned from a biota full of oddballs. However, analyses of the distribution of the Ediacaran organisms in time and space can be carried out without having to guess at the systematic position of the organisms. Combining these results with data on paleotectonics, paleoenvironmental parameters, and the ages of various assemblages sheds light on the origins, ecology, and even the systematic positions of the Ediacaran organisms. Parsimony Analysis of Endemism (PAE) confirms earlier studies in grouping Ediacaran biotas into three major clusters: the Avalon, White Sea, and Nama Assemblages. The available radiometric and stratigraphic data suggest that the Avalon is the oldest, the White Sea is next oldest, and the Nama extends to the base of the Cambrian. The "frondlike" Ediacaran taxa, and to a lesser extent the "medusoids," collectively show significantly longer stratigraphic ranges, broader geographical and paleoenvironmental ranges, and less provinciality than "bilaterian" and tubular taxa. Almost all tubular Ediacarans appear to be confined to equatorial areas, whereas other Ediacaran organisms show weak or no latitudinal diversity gradients. I conclude that the Ediacaran organisms show a diverse range of responses to various environmental parameters. There is no basis for classifying them all as having a single body plan and mode of life, as has often been done in the past.     

Glacial refugia and reticulate evolution: the case of the Tasmanian eucalypts

Tasmania is a natural laboratory for investigating the evolutionary processes of the Quaternary. It is a large island lying 40-44 degrees S, which was repeatedly glaciated and linked to southeastern continental Australia during the Quaternary. Climate change promoted both the isolation of species in glacial refugia, and an exchange between Tasmanian and mainland floras. Eucalyptus is a complex and diverse genus, which has increased in abundance in Australia over the past 100 kyr, probably in response to higher fire frequency. Morphological evidence suggests that gene flow may have occurred between many eucalypt species after changes in their distribution during the Quaternary. This paper summarizes recent genetic evidence for migration and introgressive hybridization in Tasmanian Eucalyptus. Maternally inherited chloroplast DNA reveals a long-term persistence of eucalypts in southeastern Tasmanian refugia, coupled with introgressive hybridization involving many species. Detailed analysis of the widespread species Eucalyptus globulus suggests that migration from mainland Australia was followed by introgression involving a rare Tasmanian endemic. The data support the hypothesis that changes in distribution of interfertile species during the Quaternary have promoted reticulate evolution in Eucalyptus.     

The biogeography of herbivorous arthropods: species accrual on tropical crops

ABSTRACT.

• 1 The size of range of host plants and animals has been shown repeatedly to be the best single correlate of number of associated parasite species. For a single species of host distributed over many regions, there should exist two important additional correlates: the sizes of source pools of potential colonists within regions and the distribution of the host's close relatives among regions.
• 2 Certain tropical crops are useful in examining these ideas because they are widely-cultivated and the relevant data are available. A comparison of the data for the herbivorous arthropods of cacao, citrus, coconuts, coffee, cotton, rice and sugar cane shows that regions in Amazonia, Southern Asia/Australia and sub-Saharan Africa consistently fall above species-area regression lines, whereas regions in North and South America (except Amazonia), Western Asia and Europe tend to fall below them.
• 3 The pattern implicates the importance of source pool size of potential colonists and taxonomic isolation of the host in influencing arthropod accrual.
• 4 Cultivation methods, sampling effects and latitude conceivably could also influence accrual, but their importance is questionable for the seven crop/parasite systems examined.