Species diversification and phylogeographical patterns of birds in response to the uplift of the Qinghai-Tibet Plateau and Quaternary glaciations

The Qinghai-Tibet Plateau （QTP） is well known for being of great importance in the evolution of montane species due to its unique geological history and landform configuration, climate complexity, and diversified habitats. The effect of environmental changes since the Quaternary on species diversification, population genetic structure, and demography under environmental change can be studied using phylogenetic and phylogeographieal approaches. Birds are the most well-studied group of all terrestrial vertebrates with regard to their response to climatic changes over time. Herein, we briefly review the species diversification of birds in response to the uplift of the QTP, focusing on summarizing the different phylogeographical patterns of birds on the Plateau, its southeastern margin, and the Eastern Himalayas and the reasons underlying these patterns. Speciation was found to be closely related to the uplift of the QTP, with different patterns of intraspecific processes： （1） no divergence within a single refuge was identified in a restricted semi-continuous area of the eastern margin of the Plateau; （2） two divergent lineages with separated refugia were located at the south-eastern and north-eastern margins of the plateau; and （3） multiple divergent lineages within subregions were found in the Eastern Himalayas. Glacial movements and induced climate change are considered to be key factors in shaping these different patterns. The species distributed mainly in the heavily ice-covered platform regions of the Plateau experienced population expansion following the retreat of the extensive glaciations, whereas the species distributed on the ice-free edges of the plateau maintained their population size at a stable level. Demographic stresses on the edge species might have been mitigated by the milder climate in comparison to their platform-distributed counterparts. Various behavioral and ecological characteristics, including dispersal capacity, habitat preference, and elevation specificity, along with evolutionary history might have helped to shape these different phylogeographical patterns [Current Zoology 60 （2）： 149-161, 2014].     

Competition both drives and impedes diversification in a model adaptive radiation

Competitors are known to be important in governing the outcome of evolutionary diversification during an adaptive radiation, but the precise mechanisms by which they exert their effects remain elusive. Using the model adaptive radiation of Pseudomonas fluorescens, we show experimentally that the effect of competition on diversification of a focal lineage depends on both the strength of competition and the ability of the competitors to diversify. We provide evidence that the extent of diversification in the absence of interspecific competitors depends on the strength of resource competition. We also show that the presence of competitors can actually increase diversity by increasing interspecific resource competition. Competitors that themselves are able to diversify prevent diversification of the focal lineage by removing otherwise available ecological opportunities. These results suggest that the progress of an adaptive radiation depends ultimately on the strength of resource competition, an effect that can be exaggerated or impeded by the presence of competitors.     

Lineage origin and expansion of a Neotropical migrant songbird after recent glaciation events

Birds of the Northern Hemisphere often harbour the genetic signature of postglaciation expansion but analyses identifying the location of refugia and the directionality of expansions are rare. Here we explore the evolutionary history of yellow warbler lineages, focusing on how these lineages recolonized their current range. We genotyped samples from 696 yellow warblers via direct sequencing of a 333-bp control region I mitochondrial DNA fragment or lineage-specific genotyping. Phylogenetic analysis revealed two monophyletic clades: a highly migratory group including previously identified eastern and western lineages and a less migratory group including a lineage consisting of tropical residents and a new 'southern' lineage localized in southwest United States. We then modelled the expansion of the eastern and western lineages, identified the location of potential refugia and assessed the importance of migration as a historical factor promoting gene flow. The expansion of the eastern lineage proceeded from a main refugia in the eastern United States, with possible contribution of an additional local refugia. In the western lineage, the expansion proceeded from a single refugia possibly located in western United States. Because two lineages overlapped to varying degrees in central North America, we suggest that the Canadian Prairies offered a bridge of riparian habitats where the lineages met after glacier retreat, while the US Central Great Plains acted as a barrier that limited secondary contact. Finally, gene flow was more important along the north-south axis of migration than away from it, suggesting spring migration played a role in the dispersal of lineages.     

Patterns of diversification and genetic population structure of small mammals in Taiwan

Taiwan is a mountainous island off the coast of the Asian continent. The island is located on the continental shelf and rises to an elevation of nearly 4000 m. It became an island approximately 4 million years ago and has been connected to the continent more than once since its emergence. Therefore, the elevational zonation of two Taiwanese pairs of congeners in the rodent genera Apodemus and Niviventer can be explained by one of two competing hypotheses. One hypothesis assumes that speciation of the two congeners occurred in situ after an ancestral species migrated from the continent. In contrast, the second hypothesis argues the zonation resulted from separate incursion events during the connections. The phylogenetic analyses, which are based on electrophoretic allozyme data, reject the first of these hypotheses. Furthermore, genetic population structure and gene flow of three species of Taiwanese rodents (Apodemus semotus, Niviventer culturatus and Microtus kikuchii) are studied in relation to their patterns of elevational distribution. The genetic structure of A. semotus and N. culturatus, which have extensive elevational distribution, is rather homogeneous and no genie discontinuity or cline in allele frequency was detected. Gene flow among subpopulations for these two species is rather substantial; therefore, the potential isolating effect imposed by deep river valleys is minimal. Conversely, isolation of populations of M. kikuchii on different mountaintops is quite complete as mirrored by the high level of genie differentiation and low gene flow.     

On size and area: Patterns of mammalian body size extremes across landmasses

We describe a biogeographic pattern in which mammalian body size extremes scale with landmass area. The relationship between the largest and the smallest mammal species found on different landbridge islands, mountaintops and continents shows that the size of the largest species increases, while that of the smallest species decreases, with increase in the area of the landmass. We offer two possible explanations: (1) that the pattern is the result of sampling artefacts, which we call the ‘statistical artefact hypothesis’, or (2) that the pattern is the result of processes related to the way body size affects the number of individuals that a particular species can pack in a given area, which we call the ‘area-scaling hypothesis’. Our results point out that the pattern is not a statistical artefact resulting from random sampling, but can be explained by considering the scaling of individual space requirements and its effect on population survival on landmasses of different area. This revised version was published online in July 2006 with corrections to the Cover Date.     

Understanding global patterns of mammalian functional and phylogenetic diversity

Documenting and exploring the patterns of diversity of life on Earth has always been a central theme in biology. Species richness despite being the most commonly used measure of diversity in macroecological studies suffers from not considering the evolutionary and ecological differences among species. Phylogenetic diversity (PD) and functional diversity (FD) have been proposed as alternative measures to overcome this limitation. Although species richness, PD and FD are closely related, their relationships have never been investigated on a global scale. Comparing PD and FD with species richness corroborated the general assumptions of surrogacy of the different diversity measures. However, the analysis of the residual variance suggested that the mismatches between the diversity measures are influenced by environmental conditions. PD increased relative to species richness with increasing mean annual temperature, whereas FD decreased with decreasing seasonality relative to PD. We also show that the tropical areas are characterized by a FD deficit, a phenomenon, that suggests that in tropical areas more species can be packed into the ecological space. We discuss potential mechanisms that could have resulted in the gradient of spatial mismatch observed in the different biodiversity measures and draw parallels to local scale studies. We conclude that the use of multiple diversity measures on a global scale can help to elucidate the relative importance of historical and ecological processes shaping the present gradients in mammalian diversity.     

Persistence and diversification of the Holarctic shrew,Sorex tundrensis (Family Soricidae), in response to climate change

Environmental processes govern demography, species movements, community turnover and diversification and yet in many respects these dynamics are still poorly understood at high latitudes. We investigate the combined effects of climate change and geography through time for a widespread Holarctic shrew, Sorex tundrensis. We include a comprehensive suite of closely related outgroup taxa and three independent loci to explore phylogeographic structure and historical demography. We then explore the implications of these findings for other members of boreal communities. The tundra shrew and its sister species, the Tien Shan shrew (Sorex asper), exhibit strong geographic population structure across Siberia and into Beringia illustrating local centres of endemism that correspond to Late Pleistocene refugia. Ecological niche predictions for both current and historical distributions indicate a model of persistence through time despite dramatic climate change. Species tree estimation under a coalescent process suggests that isolation between populations has been maintained across timeframes deeper than the periodicity of Pleistocene glacial cycling. That some species such as the tundra shrew have a history of persistence largely independent of changing climate, whereas other boreal species shifted their ranges in response to climate change, highlights the dynamic processes of community assembly at high latitudes.     

Elongation of palindromic repetitive DNA by DNA polymerase from hyperthermophilic archaea: a mechanism of DNA elongation and diversification

DNA polymerase from hyperthermophilic bacteria can elongate tandem repetitive oligoDNA with a complete or incomplete palindromic sequence under isothermal conditions by "hairpin elongation". However, the product of the reaction has not yet been sufficiently characterized. Here, I demonstrate that when palindromic repetitive oligoDNA, e.g., (5'AGATATCT3')(6), was added as a "seed" to the DNA synthesis reaction catalyzed by DNA polymerase from the archaea Thermococcus litoralis (Vent polymerase) at 74 degrees C, the product was (5'AGATATCT3')(n). The product itself was palindromic and repetitive, and its motif (unit) sequence was exactly the same as that of the seed oligoDNA. On the other hand, when a pseudopalindrome, which contains a palindrome-breaking nucleotide (underlined), was present in seed oligoDNA, e.g., (5'GATTC3')(6), the product was (5'GATATC3')(n), which had a different motif sequence from that of the seed oligoDNA. When a pseudopalindrome (5'AGATATCA3')(6) was added to the reaction, the products were 5'TATCA . (AGATATCA)(3) . AGATATCT . (TGATATCT)(5) . TGATA3', etc. When 5'AGATATCA . (AGATATCT3')(5) was added, products were 5'TATCT . (AGATATCT)(2).TGATATCT . AGATATCT . AGATATCA . AGATATCT . AGA3', etc., demonstrating the generation of many "mutations" in the product DNA. I conclude that a tandem repetitive sequence is faithfully elongated (amplified) by hyperthermophilic DNA polymerase if it is completely palindromic, but is elongated with many errors if it is incompletely palindromic (pseudopalindromic) or mixed with a pseudopalindrome. The results suggest a protein-catalyzed elongation/diversification mechanism of short repetitive DNAs on the early earth.     

Comparative proteomics reveals evidence for evolutionary diversification of rodent seminal fluid and its functional significance in sperm competition

During insemination, males of internally fertilizing speciestransfer a complex array of seminal fluid proteins to the femalereproductive tract. These proteins can have profound effectson female reproductive physiology and behavior and are thoughtto mediate postcopulatory sexual selection and intersexual conflict.Such selection may cause seminal fluid to evolve rapidly, withpotentially important consequences for speciation. Here we investigatethe evolution of seminal fluid proteins in a major mammalianradiation, the muroid rodents, by quantifying diversity in seminalfluid proteome composition for the first time across a broadrange of closely related species. Using comparative proteomicstechniques to identify and cross-match proteins, we demonstratethat rodent seminal fluid is highly diverse at the level ofboth proteomes and individual proteins. The striking interspecificheterogeneity in seminal fluid composition revealed by our surveyfar exceeds that seen in a second proteome of comparable complexity,skeletal muscle, indicating that the complement of proteinsexpressed in seminal fluid may be subject to rapid diversification.We further show that orthologous seminal fluid proteins exhibitsubstantial interspecific variation in molecular mass. Becausethis variation cannot be attributed to differential glycosylationor radical differences in termination sites, it is stronglysuggestive of rapid amino acid divergence. Sperm competitionis implicated in generating such divergence for at least onemajor seminal fluid protein in our study, SVS II, which is responsiblefor copulatory plug formation via transglutaminase-catalyzedcross-linking after insemination. We show that the molecularmass of SVS II is positively correlated with relative testissize across species, which could be explained by selection foran increased number of cross-linking sites involved in the formationof the copulatory plug under sperm competition.     

Historical biogeography and evolutionary diversification of Lilium(Liliaceae): New insights from plastome phylogenomicsOA

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium(14plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a timecalibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic act...     

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

Understanding the evolutionary history of the species in a particular region provides insights into how that fauna was formed. Of particular interest to biogeographers is examining the impact a geographical barrier had in generating temporal genetic diversity among codistributed species. We examined the impact a major New World barrier, the Isthmus of Tehuantepec (IT) in southern Mexico, had on a regional bird fauna. Specifically, genetic data from 10 montane-forest bird taxa were analysed using approximate Bayesian computation (ABC) to test the hypothesis of simultaneous intraspecific diversification at the IT. Because effective population size (N_e) has the greatest impact on coalescent times, thereby affecting tests of divergence among codistributed taxa, we chose priors for both current and ancestral N_e using empirical estimates of theta. The ABC method detected two discrete diversification events. Subsequent analysis with the number of diversification events constrained to two suggests that four taxa diverged in an older event, with the remaining six diverging more recently. Application of a range of mutation rates from 2.0 to 5.0% Myr⁻¹ places both events within the Pleistocene or Late Pliocene, suggesting that fluctuations in montane habitat induced by climate cycles and a late Pliocene seaway may have fractured this montane bird fauna. The results presented here suggest this avian fauna responded in a relatively concerted fashion over the last several million years.     

Trait-dependent diversification and the impact of palaeontological data on evolutionary hypothesis testing in New World ratsnakes (tribe Lampropeltini)

For studies investigating trait evolution, there are at least two important questions. First, have traits under consideration influenced cladogenesis and extinction in the group? Second, how do fossil data alter inferences about trait evolution or diversification‐rate dynamics? However, relatively few studies have assessed these questions. Here, we use recently developed methods to test for trait‐dependent diversification in the New World colubrid snake tribe Lampropeltini. We also integrate data from fossil taxa into phylogenetic estimation of evolutionary parameters using a simple Monte Carlo randomization test. These analyses suggest that ecological conditions in temperate regions are tied to higher rates of cladogenesis, but that body size is not related to diversification in the group. We also find that the inclusion of fossil taxa alters absolute estimates of size and the rate of size evolution, but not the overall pattern of ecomorphological diversification, as well as estimates of evolutionary rates, particularly extinction.     

Divergence in foraging behavior of foliage-gleaning birds of Canadian and Russian boreal forests

We compared foraging behavior of foliage-gleaning birds of the boreal forest of two Palaearctic (central Siberia and European Russia) and two Nearctic (Mackenzie and Ontario, Canada) sites. Using discriminant function analysis on paired sites we were able to distinguish foliage-gleaning species from the Nearctic and Palaearctic with few misclassifications. The two variables that most consistently distinguished species of the two avifaunas were the percentage use of conifer foliage and the percentage use of all foliage. Nearctic foliage-gleaner assemblages had more species that foraged predominantly from coniferous foliage and displayed a greater tendency to forage from foliage, both coniferous and broad-leafed, rather than twigs, branches, or other substrates. The greater specialization on foliage and, in particular, conifer foliage by New World canopy foliage insectivores is consistent with previously proposed hypotheses regarding the role of Pleistocene vegetation history on ecological generalization of Eurasian species. Boreal forest, composed primarily of spruce and pine, was widespread in eastern North America, whereas pockets of forest were scattered in Eurasia (mostly the mountains of southern Europe and Asia). This may have affected the populations of birds directly or indirectly through reduction in the diversity and abundance of defoliating outbreak insects. Loss of habitat and resources may have selected against ecological specialization on these habitats and resources. Received: 11 May 1998 / Accepted: 24 June 1999     

The impact of Pleistocene climate change on an ancient arctic-alpine plant: multiple lineages of disparate history in Oxyria digyna

The ranges of arctic-alpine species have shifted extensively with Pleistocene climate changes and glaciations. Using sequence data from the trnH-psbA and trnT-trnL chloroplast DNA spacer regions, we investigated the phylogeography of the widespread, ancient (>3 million years) arctic-alpine plant Oxyria digyna (Polygonaceae). We identified 45 haplotypes and six highly divergent major lineages; estimated ages of these lineages (time to most recent common ancestor, T(MRCA)) ranged from ～0.5 to 2.5 million years. One lineage is widespread in the arctic, a second is restricted to the southern Rocky Mountains of the western United States, and a third was found only in the Himalayan and Altai regions of Asia. Three other lineages are widespread in western North America, where they overlap extensively. The high genetic diversity and the presence of divergent major cpDNA lineages within Oxyria digyna reflect its age and suggest that it was widespread during much of its history. The distributions of individual lineages indicate repeated spread of Oxyria digyna through North America over multiple glacial cycles. During the Last Glacial Maximum it persisted in multiple refugia in western North America, including Beringia, south of the continental ice, and within the northern limits of the Cordilleran ice sheet. Our data contribute to a growing body of evidence that arctic-alpine species have migrated from different source regions over multiple glacial cycles and that cryptic refugia contributed to persistence through the Last Glacial Maximum.     

Phylogeography of the Percichthyidae (Pisces) in Patagonia: roles of orogeny, glaciation, and volcanism

We used molecular evidence to examine the roles that vicariance mechanisms (mountain-building and drainage changes during the Pleistocene) have played in producing phylogeographical structure within and among South American fish species of the temperate perch family Percichthyidae. The percichthyids include two South American genera, Percichthys and Percilia, each containing several species, all of which are endemic to southern Argentina and Chile (Patagonia). Maximum-likelihood phylogenies constructed using mitochondrial DNA (mtDNA) control region haplotypes and nuclear GnRH3-2 intron allele sequences support the current taxonomy at the genus level (both Percichthys and Percilia form strongly supported, monophyletic clades) but indicate that species-level designations need revision. Phylogeographical patterns at the mtDNA support the hypothesis that the Andes have been a major barrier to gene flow. Most species diversity occurs in watersheds to the west of the Andes, together with some ancient divergences among conspecific populations. In contrast, only one species (Percichthys trucha) is found east of the Andes, and little to no phylogeographical structure occurs among populations in this region. Mismatch analyses of mtDNA sequences suggest that eastern populations last went through a major bottleneck c. 188 000 bp, a date consistent with the onset of the penultimate and largest Pleistocene glaciation in Patagonia. We suggest that eastern populations have undergone repeated founder-flush events as a consequence of glacial cycles, and that the shallow phylogeny is due to mixing during recolonization periods. The area of greater diversity west of the Andes lies outside the northern limit of the glaciers. mtDNA mismatch analysis of the genus Percilia which is restricted to this area suggests a long-established population at equilibrium. We conclude that patterns of genetic diversity in these South American genera have been primarily influenced by barriers to gene flow (Andean orogeny, and to a lesser extent, isolation in river drainages), and by glacial cycles, which have resulted in population contraction, re-arrangement of some watersheds, and the temporary breakdown of dispersal barriers among eastern river systems.     

Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins

Understanding the determinants of the rate of protein sequenceevolution is of fundamental importance in evolutionary biology.Many recent studies have focused on the yeast because of theavailability of many genome-wide expressional and functionaldata. Yeast studies revealed a predominant role of gene expressionlevel and a minor role of gene essentiality in determining therate of protein sequence evolution. Whether these rules applyto complex organisms such as mammals is unclear. Here we assemblea list of 1,138 essential and 2,341 nonessential mouse genesbased on targeted gene deletion experiments and report a significantimpact of gene essentiality on the rate of mammalian proteinevolution. Gene expression level has virtually no effect, althoughtissue specificity in expression pattern has a strong influence.Unexpectedly, gene compactness, measured by average intron sizeand untranslated region length, has the greatest influence.Hence, the relative importance of the various factors in determiningthe rate of mammalian protein evolution is gene compactness> gene essentiality tissue specificity > expression level.Our results suggest a considerable variation in rate determinantsbetween unicellular organisms such as the yeast and multicellularorganisms such as mammals.     

Demographic constraints in evolution: Towards unifying the evolutionary theories of senescence and niche conservatism

Summary I suggest that there may be a fundamental conceptual unity between two seemingly disparate phenomena: (1) senescence (the progressive deterioration in physiological function and, thus, individual fitness with age) and (2) niche conservatism (the observation that species often seem rather fixed over evolutionary time in their basic niche properties). I argue that both phenomena arise from demographic asymmetries. The evolutionary theory of ageing rests on the observation that the force of selection declines with age, reflecting the basic demographic facts that in persistent populations there are always fewer individuals in old than in young age classes and these individuals tend to have lower reproductive value. A similar demographic asymmetry arises when populations inhabit environments with source habitats (i.e. where conditions are within the species' niche) and sink habitats (where conditions lie outside the niche): there tend to be more individuals in sources than in sinks and individuals in sources have relatively higher reproductive values. These demographic asymmetries should often imply that the force of selection is greater in sources than in sinks, leading automatically towards niche conservatism. I suggest that niche evolution is most likely in circumstances where these demographic asymmetries in space weaken or reverse.