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.     

The Paleogene fossil record of birds in Europe

The Paleogene (Paleocene-Oligocene) fossil record of birds in Europe is reviewed and recent and fossil taxa are placed into a phylogenetic framework, based on published cladistic analyses. The pre-Oligocene European avifauna is characterized by the complete absence of passeriform birds, which today are the most diverse and abundant avian taxon. Representatives of small non-passeriform perching birds thus probably had similar ecological niches before the Oligocene to those filled by modern passerines. The occurrence of passerines towards the Lower Oligocene appears to have had a major impact on these birds, and the surviving crown-group members of many small arboreal Eocene taxa show highly specialized feeding strategies not found or rare in passeriform birds. It is detailed that no crown-group members of modern 'families' are known from pre-Oligocene deposits of Europe, or anywhere else. The phylogenetic position of Paleogene birds thus indicates that diversification of the crown-groups of modern avian 'families' did not take place before the Oligocene, irrespective of their relative position within Neornithes (crown-group birds). The Paleogene fossil record of birds does not even support crown-group diversification of Galliformes, one of the most basal taxa of neognathous birds, before the Oligocene, and recent molecular studies that dated diversification of galliform crown-group taxa into the Middle Cretaceous are shown to be based on an incorrect interpretation of the fossil taxa used for molecular clock calibrations. Several taxa that occur in the Paleogene of Europe have a very different distribution than their closest extant relatives. The modern survivors of these Paleogene lineages are not evenly distributed over the continents, and especially the great number of taxa that are today restricted to South and Central America is noteworthy. The occurrence of stem-lineage representatives of many taxa that today have a restricted Southern Hemisphere distribution conflicts with recent hypotheses on a Cretaceous vicariant origin of these taxa, which were deduced from the geographical distribution of the basal crown-group members.     

A South American snake lineage from the Eocene Greenhouse of North America and a reappraisal of the fossil record of “anilioid” snakes

“Anilioidea” is a likely paraphyletic assemblage of pipe snakes that includes extant Aniliidae from equatorial South America, Uropeltoidea from South and Southeast Asia, and a fossil record that consists primarily of isolated precloacal vertebrae ranging from the earliest Late Cretaceous and includes geographic distributions in North America, South America, Europe, and Africa. Articulated precloacal vertebrae from the middle Eocene Bridger Formation of Wyoming, attributed to Borealilysia nov. gen., represent an unambiguous North American aniliid record and prompts a reconsideration of described pipe snakes and their resultant biogeographic histories. On the basis of vertebral apomorphies, the vast majority of reported fossils cannot be assigned to “Anilioidea”. Instead, most records represent stem taxa and macrostomatans erroneously assigned to anilioids on the basis of generalized features associated with fossoriality. A revised fossil record demonstrates that the only extralimital distributions of fossil “anilioids” consist of the North American aniliid record, and there is no unambiguous fossil record of Old World taxa. The occurrence of aniliids in the mid-high latitudes of the late early Eocene of North America is consistent with histories of northward shifts in equatorial ecosystems during the early Paleogene Greenhouse.     

Avian higher level biogeography: Southern Hemispheric origins or Southern Hemispheric relicts?

A recent analysis of a comprehensive phylogenetic data set suggested Southern Hemispheric origins for various higher level taxa of neornithine (crown group) birds. These results contrast with hypotheses derived from the fossil record, with the occurrence of successively branching stem group representatives of many “Southern Hemispheric” bird groups in the early Cenozoic of Europe and North America suggesting relict extant distributions. However, a selective consideration of the fossil record and the merging of extant ranges may have resulted in a skewed picture of the past biogeographical history of birds. For future studies, it is proposed that multiple taxa of successively branching Northern Hemispheric stem group representatives are considered to narrow down the ancestral areas of the crown group representatives.     

Fossils of the Fagaceae and their implications in systematics and biogeography

The fossil history of the Fagaceae from China and its systematic and biogeographic implications are discussed based on revisionary studies of the fossil records. No creditable macrofossil record of the Fagaceae exists in the Cretaceous deposits and all the Cretaceous microfossil reports remain equivocal and require further study. The Paleocene fossils show the appearance and diversification of the two groups corresponding to the subfamilies Fagoideae and Castaneoideae sensu Nixon. By the Eocene, all modern genera had been present. The oldest fagaceous fossils represent subfamily Fagoideae with affinities to the extant genus Trigonobalanus. The leaf fossil genus Berryophyllum, with affinities to Quercus subg. Cyclobalanopsis, has been documented by the early Eocene and might have occurred earlier than other fossils assignable to Quercus. The appearance of evergreen sclerophyllous Ouercus with entire leaves might have occurred earlier than those with toothed leaves. Deciduous, urticoid-leaved oak fossils (Quercus subg. Quercus sect. Quercus) had not appeared until the Miocene. Fossil equivalents of Trigonobalanus, Castanopsis and Lithocarpus had occurred in Europe and North America by the early Tertiary, suggesting that continuous distributions were achieved via the northern hemisphere land bridges. Three groups of evergreen sclerophyllous oaks of apparent close phylogenetic relationships occurred in the Hengduan mountains, the Mediterranean area and northwestern North America. Their fossil forms have become dominant elements of those vegetation zones since the Miocene. A shared fossil history indicates a possible biogeographic boundary formed by the ancient Mediterranean. The evidence suggests that the oaks might arrive in North America during two distinct geologic periods: evergreen sclerophyllous entire-leaved oaks appeared by the Early Tertiary, whereas thedeciduous oaks with urticoid leaves appeared in the Late Tertiary.     

The mahogany family "out-of-Africa": divergence time estimation, global biogeographic patterns inferred from plastid rbcL DNA sequences, extant, and fossil distribution of diversity

With information on fossils and extant distribution of diversity/endemism in the mahogany family, we perform a global biogeographic study of Meliaceae using plastid rbcL data for all subfamilies, tribes and nearly all genera. Our study indicates that: (1) Meliaceae are of western Gondwanan origin; (2) dispersal played an important role for the current distribution of mahogany biota; and (3) the direction of dispersal was most likely an "out-of-Africa" scenario with important dispersal routes across Eurasia and between Eurasia and North America provided by Beringia and the North Atlantic land bridge and North America and South America via island chains and/or direct land connections. Populations in North America, Europe, and East Asia were presumably eliminated as tropical climates disappeared from these areas during the Miocene. Extensive Meliaceae fossil findings confirm that the entry of megathermal (frost-intolerant) angiosperms into southern continents from Oligocene to Pliocene must be considered as an important means of establishing pantropical distribution patterns.     

内蒙古中始新世一似ameghinornithid鸟类(鸟纲:Cariamae:Ameghinornithidae?)

内蒙古二连盆地额尔登敖包剖面(相当于伊尔丁曼哈组)的中始新世早期地层中新发现的一件标本显示其属于一个与ameghinornithid相似的种,代表了Ameghinomithidae在亚洲的首个记录.新标本具有外踝半圆形,缺失骨质腱桥,伸肌沟外侧具有大而平的结节,以及其他与ameghinomithid和似ameghinomithid鸟类共有的特征.内蒙古标本与欧洲最古老的ameghinomithids记录大体属同一时代(约48 Ma).与同时期内蒙古哺乳动物群主要由亚洲类群组成兼有少量与北美有关的绝灭类群不同,这类鸟类中始新世时在北美缺失,而存在于欧洲和亚洲.加上埃及法尤姆早渐新世地层中发现的似ameghinomithid鸟类,这类已经绝灭的鸟类的地理分布似乎比过去所认为的要广泛得多.     

Tracing the patterns of non-marine turtle richness from the Triassic to the Palaeogene: from origin to global spread

Turtles are key components of modern vertebrate faunas and their diversity and distributions are likely to be affected by anthropogenic climate change. However, there is limited baseline data on turtle taxonomic richness through time or assessment of their past responses to global environmental change. We used the extensive Triassic–Palaeogene (252–223 Ma) fossil record of terrestrial and freshwater turtles to investigate diversity patterns, finding substantial variation in richness through time and between continents. Globally, turtle richness was low from their Triassic origin until the Late Jurassic. There is strong evidence for high richness in the earliest Cretaceous of Europe, becoming especially high following the Cretaceous Thermal Maximum and declining in all continents by the end-Cretaceous. At the K–Pg boundary, South American richness levels changed little while North American richness increased, becoming very high during the earliest Palaeogene (Danian). Informative data are lacking elsewhere for this time period. However, the Selandian–Thanetian interval, approximately 5 myr after the K–Pg mass extinction, shows low turtle richness in Asia, Europe and South America, suggesting that the occurrence of exceptional turtle richness in the post-extinction Paleocene fauna of North America is not globally representative. Richness decreased over the Eocene–Oligocene boundary in North America but increased to its greatest known level for Europe, implying very different responses to dramatic climatic shifts. Time series regressions suggest number of formations sampled and palaeotemperature are the primary influencers of face-value richness counts, but additional factors not tested here may also be involved.     

From Europe to America: pliocene to recent trans-atlantic expansion of cold-water north atlantic molluscs

Data on the geographical distribution, phylogeny and fossil record of cool-temperate North Atlantic shell-bearing molluscs that live in waters shallower than 100 m depth belong to two biogeographic provinces, one in eastern North America north of Cape Cod, the other in northern Europe. Amphi-Atlantic species, which are found in both provinces, comprise 30.8% of the 402 species in the northeastern Atlantic and 47.3% of the 262 species in the northwestern Atlantic. Some 54.8% of these amphi-Atlantic species have phylogenetic origins in the North Pacific. Comparisons among fossil Atlantic faunas show that amphi-Atlantic distributions became established in the Middle Pliocene (about 3.5 million years ago), and that all represent westward expansions of European taxa to North America. No American taxa spread eastward to Europe without human assistance. These results are in accord with previous phylogeographic studies among populations within several amphi-Atlantic species. Explanations for the unidirectional expansion of species across the Atlantic remain uncertain, but may include smaller size and greater prior extinction of the North American as compared to the European fauna and biased transport mechanisms. Destruction of the European source fauna may jeopardize faunas on both sides of the Atlantic.     

The Great American Biotic Interchange in frogs: multiple and early colonization of Central America by the South American genus Pristimantis (Anura: Craugastoridae)

The completion of the land bridge between North and South America approximately 3.5-3.1 million years ago (Ma) initiated a tremendous biogeographic event called the Great American Biotic Interchange (GABI), described principally from the mammalian fossil record. The history of biotic interchange between continents for taxonomic groups with poor fossil records, however, is not well understood. Molecular and fossil data suggest that a number of plant and animal lineages crossed the Isthmus of Panama well before 3.5 Ma, leading biologists to speculate about trans-oceanic dispersal mechanisms. Here we present a molecular phylogenetic analysis of the frog genus Pristimantis based on 189 individuals of 137 species, including 71 individuals of 31 species from Panama and Colombia. DNA sequence data were obtained from three mitochondrial (COI, 12S, 16S) and two nuclear (RAG-1 and Tyr) genes, for a total of 4074 base pairs. The resulting phylogenetic hypothesis showed statistically significant conflict with most recognized taxonomic groups within Pristimantis, supporting only the rubicundus Species Series, and the Pristimantis myersi and Pristimantis pardalis Species Groups as monophyletic. Inference of ancestral areas based on a likelihood model of geographic range evolution via dispersal, local extinction, and cladogenesis (DEC) suggested that the colonization of Central America by South American Pristimantis involved at least 11 independent events. Relaxed-clock analyses of divergence times suggested that at least eight of these invasions into Central America took place prior to 4 Ma, mainly in the Miocene. These findings contribute to a growing list of molecular-based biogeographic studies presenting apparent temporal conflicts with the traditional GABI model.     

壳斗科的地质历史及其系统学和植物地理学意义

在收集整理现有壳斗科化石资料的基础上,讨论了壳斗科及其各属的起源时间、地史分布和地史 演替过程以及这些化石资料在系统学和植物地理学上的意义。白垩纪尚无壳斗科可靠的大化石记录, 微化石需要进一步研究才能确定亲缘关系以及古新世壳斗科已经分化出两个类群。从以上这些事实推 论壳斗科起源于白垩纪晚期,而壳斗科现代各属出现的时间应不晚于古新世。最早发现的壳斗科化石和现代栗亚科和水青冈亚科在形态结构上非常相似,这一事实表明,壳斗科分为两个亚科的观点更接近客观事实。在水青冈亚科中,三棱栎类的化石最早出现;在栎属中,青冈亚属更接近祖先类群;在地史中全缘栎类较具齿栎类出现早,粗齿的落叶栎类出现最晚。三棱栎属、栲属和石栎属的化石在老第三纪出现于北美和欧洲的事实说明,北美、欧洲和东亚在老第三纪时有一个相通的壳斗科植物区系。南美的三棱栎是通过北美进入南美的。中国横断山、欧洲地中海沿岸和北美西北部有一类形态特征相似、亲缘关系相近的硬叶栎类,它们之间有相同的地质演替历史,它们现代分布边界可能就是古地中海的边界。美洲的栎类有两个来源,常绿硬叶栎类是通过古地中海沿岸而经北美-欧洲陆桥到达的,落叶栎类则是在中新世以后通过白令海峡到达的。     

ORIGINS AND RELATIONSHIPS OF TROPICAL NORTH AMERICA IN THE CONTEXT OF THE BOREOTROPICS HYPOTHESIS

The boreotropics hypothesis postulates a preferential tropical biotic interchange between North America and Eurasia during the early Tertiary that was directed by Eocene thermal maxima and the close proximity of these two continental plates. This preferential interchange occurred at a time when South America was geologically and biotically isolated. A prediction of this hypothesis posits that a taxon with a present-day center of diversity in tropical North America, and with an early Tertiary fossil record from any region there, has a high probability of having sister-group relatives in the Paleotropics and derived relatives in South America. We propose a test of this prediction with phylogenetic studies of two pantropical taxa of Leguminosae that have early Tertiary North American fossil records. Our findings are consistent with the boreotropics hypothesis, and additional evidence suggests that many tropical elements in North America could be descendants of northern tropical progenitors. Ramifications of this hypothesis include the importance of integrating the fossil record with cladistic biogeographic studies, theoretical bases for recognizing tropical taxa with such disjunct distributions as Mexico and Madagascar, identification of taxa that may be most useful for testing vicariance models of Caribbean biogeography, and integrating the study of disjunct distributions in temperate regions of the northern hemisphere with those in the neo- and paleotropics.     

Evidence of carpinus (betulaceae) in the late tertiary (pliocene) of alabama

Carpinus is a common and widespread element of the modern North American forest vegetation, but its scant fossil record on the continent is perplexing, especially considering the abundant and relatively continuous record of the genus in the Tertiary of Europe and Asia. Despite earlier claims of Tertiary Carpinus remains, recent reviews have indicated that a definitive post-Eocene Tertiary record of the genus in North America is lacking. Therefore, it remains uncertain if Carpinus was present but left no clear fossil record or if the genus became extinct in North America and migrated back to the continent more recently. A reinvestigation of the Citronelle Formation paleoflora has yielded conclusive evidence for the presence of Carpinus in the Gulf Coastal Plain of Alabama during the Pliocene based upon the discovery of a nutlet bract. Carpinus bracts are distinctive and consist of a central bract fused basally with two lateral bractlets. This specimen provides proof of the existence of Carpinus on this continent by the Pliocene Epoch, and any future research on the biogeography of the genus must consider this as the earliest, post-Eocene record of the genus in North America based on unequivocal reproductive structures.     

Phanerozoic marine diversity: rock record modelling provides an independent test of large-scale trends

Sampling bias created by a heterogeneous rock record can seriously distort estimates of marine diversity and makes a direct reading of the fossil record unreliable. Here we compare two independent estimates of Phanerozoic marine diversity that explicitly take account of variation in sampling—a subsampling approach that standardizes for differences in fossil collection intensity, and a rock area modelling approach that takes account of differences in rock availability. Using the fossil records of North America and Western Europe, we demonstrate that a modelling approach applied to the combined data produces results that are significantly correlated with those derived from subsampling. This concordance between independent approaches argues strongly for the reality of the large-scale trends in diversity we identify from both approaches.     

Interactions within and between clades shaped the diversification of terrestrial carnivores

A longstanding debate in evolutionary biology and paleontology is whether ecological interactions such as competition impose diversity dependence on speciation and extinction rates. Here, we analyze the fossil record of terrestrial mammalian carnivores in North America and Eurasia using a Bayesian framework to assess whether their diversity dynamics were affected by diversity dependence within and between families (12 in Eurasia, 10 in North America). We found eight instances of within‐clade diversity dependence suppressing speciation rates and detected between‐clade effects increasing extinction rates in six instances. Diversity dependence often involved lineages that migrated between continents and we found that speciation was more responsive to diversity changes within the clade, whereas extinction responded to diversity of taxa in other clades. The analysis of the fossil record of Carnivora suggests that interactions within and between clades are associated with different speciation and extinction regimes, opening room for a broader theory of diversity dependence.     

Historical biogeography of the lineage Atopochara trivolvis PECK 1941 (Cretaceous Charophyta)

The evolutionary species Atopochara trivolvis represents a unique case of a charophyte with a well-documented, long-lasting fossil record of biostratigraphical interest and a worldwide distribution. This provides an excellent basis for analysing the historical biogeography of this important species. The origin of the lineage is recorded in the Early Berriasian of Western Europe, where an archipelago-like palaeogeography would have favoured allopatric speciation and small-sized original biogeographic ranges. The species first reached Eastern Europe during the Valanginian and expanded to China during the Hauterivian. It expanded worldwide during the Barremian–Aptian, first colonizing North Africa and South America through the Guinea Corridor and subsequently reaching North America. The Barremian–Aptian worldwide expansion was probably facilitated by the monoecious nature of A. trivolvis, which allowed for long-distance animal dispersal, as is the case with extant Chara. An initial fragmentation in the biogeographic range of A. trivolvis can be detected in the Albian–Cenomanian, when the species displayed up to 5 different morphotypes in scattered localities of Eurasia and North America. During the Turonian sea-level highstand A. trivolvis became extinct also from most of these localities, while, in the Latest Cretaceous plesiomorphic populations of A. trivolvis ulanensis survived in Mongolia and Northern China. The species became completely extinct near the K/T boundary.     

Exceptionally preserved North American Paleogene metatherians: adaptations and discovery of a major gap in the opossum fossil record

A major gap in our knowledge of the evolution of marsupial mammals concerns the Paleogene of the northern continents, a critical time and place to link the early history of metatherians in Asia and North America with the more recent diversification in South America and Australia. We studied new exceptionally well-preserved partial skeletons of the Early Oligocene fossil Herpetotherium from the White River Formation in Wyoming, which allowed us to test the relationships of this taxon and examine its adaptations. Herpetotheriidae, with a fossil record extending from the Cretaceous to the Miocene, has traditionally been allied with opossums (Didelphidae) based on fragmentary material, mainly dentitions. Analysis of the new material reveals that several aspects of the cranial and postcranial anatomy, some of which suggests a terrestrial lifestyle, distinguish Herpetotherium from opossums. We found that Herpetotherium is the sister group to the crown group Marsupialia and is not a stem didelphid. Combination of the new palaeontological data with molecular divergence estimates, suggests the presence of a long undocumented gap in the fossil record of opossums extending some 45Myr from the Early Miocene to the Cretaceous.     

High migration rates shape the postglacial history of amphi‐Atlantic bryophytes

Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi‐Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best‐fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi‐Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans‐Atlantic geographic framework.