Phylogeny of the North American catfish family Ictaluridae (Teleostei: Siluriformes) combining morphology,genes and fossils

We performed the first combined‐data phylogenetic analysis of ictalurids including most living and fossil species. We sampled 56 extant species and 16 fossil species representing outgroups, the seven living genera, and the extinct genus ?Astephus long thought to be an ictalurid. In total, 209 morphological characters were curated and illustrated in MorphoBank from published and original work, and standardized using reductive coding. Molecular sequences harvested from GenBank for one nuclear and four mitochondrial genes were combined with the morphological data for total evidence analysis. Parsimony analysis recovers a crown clade Ictaluridae composed of seven living genera and numerous extinct species. The oldest ictalurid fossils are the Late Eocene members of Ameiurus and Ictalurus. The fossil clade ?Astephus placed outside of Ictaluridae and not as its sister taxon. Previous morphological phylogenetic studies of Ictaluridae hypothesized convergent evolution of troglobitic features among the subterranean species. In contrast, we found morphological evidence to support a single clade of the four troglobitic species, the sister taxon of all ictalurids. This result holds whether fossils are included or not. Some previously published clock‐based age estimates closely approximate our minimum ages of clades.     

Maximum body size in a radiating clade as a function of time

The behavior of the maximum body size (body length) in an evolving clade is exemplified by the evolutionary histories of Bivalvia, Cetacea, and Camerata (Crinoidea). Changes of the maximum size with time track closely diversification history: when a clade diversifies exponentially, the maximum size also increases exponentially, and when the number of species changes irregularly (at varying rates), the maximum size also changes in that manner. However, within any given clade, the maximum body size changes at lower rates than diversity does. The observed shifts in maximum body size approximate the rate of diversification per unit of time to the power of about 0.5.     

The phylogenetic relationships among non-diplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi: Siluriformes)

The relationships among families of catfishes are poorly understood and have yet to be the subject of a comprehensive investigation with molecular data. Existing phylogenetic hypotheses are based on morphological data and incompletely resolved. This study analyzed complete sequences of mitochondrial gene cytochrome b for 170 species from 29 of 33 extant families, and focused on the relationships of Ictaluridae to other catfishes. In addition to previous phylogenetic studies, the fossil record, paleogeography, biogeography, and distribution of extant catfish families collectively suggest the location (if extant) of the ictalurid sister taxon to be Northern or Eastern Asia. Of the extant catfishes currently native to this area and included in this analysis, parsimony and Bayesian likelihood analyses recovered Cranoglanis bouderius as the most proximal sister taxon of Ictaluridae. Seemingly, ictalurids and cranoglanidids represent another biogeographic component linking freshwater fishes of North America and eastern Asia, e.g., catostomids and paddlefishes. The results coupled with present-day catfish distributions and inferences from the fossil record collectively suggest the ancestor of Ictaluridae to have invaded freshwaters of North America at the close of the Cretaceous through northeastern Asia and northwestern North America. Other superfamilial nodes supported the results of previous phylogenetic studies of narrower taxonomic scope. Several novel relationships were recovered (including a clade composed of Pimelodidae, Pseudopimelodidae, and Heptapteridae) and these along with sources of systematic error are discussed. A broad sampling of Bagridae permitted an examination of intergeneric relationships within this family and in light of recent morphological and molecular studies.     

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on geno...     

Male-male competition and repeated evolution of terrestrial breeding in Atlantic Coastal Forest frogs*

Terrestrial breeding is a derived condition in frogs, with multiple transitions from an aquatic ancestor. Shifts in reproductive mode often involve changes in habitat use, and these are typically associated with diversification in body plans, with repeated transitions imposing similar selective pressures. We examine the diversification of reproductive modes, male and female body sizes, and sexual size dimorphism (SSD) in the Neotropical frog genera Cycloramphus and Zachaenus, both endemic to the Atlantic rainforest of Brazil. Species in this clade either breed in rocky streams (saxicolous) or in terrestrial environments, allowing us to investigate reproductive habitat shifts. We constructed a multilocus molecular phylogeny and inferred evolutionary histories of reproductive habitats, body sizes, and SSD. The common ancestor was small, saxicolous, and had low SSD. Terrestrial breeding evolved independently three times and we found a significant association between reproductive habitat and SSD, with shifts to terrestrial breeding evolving in correlation with decreases in male body size, but not female body size. Terrestrial breeding increases the availability of breeding sites and results in concealment of amplexus, egg-laying, and parental care, therefore reducing male-male competition at all stages of reproduction. We conclude that correlated evolution of terrestrial reproduction and small males is due to release from intense male-male competition that is typical of exposed saxicolous breeding.     

The evolution of mammal body sizes: responses to Cenozoic climate change in North American mammals

Explanations for the evolution of body size in mammals have remained surprisingly elusive despite the central importance of body size in evolutionary biology. Here, we present a model which argues that the body sizes of Nearctic mammals were moulded by Cenozoic climate and vegetation changes. Following the early Eocene Climate Optimum, forests retreated and gave way to open woodland and savannah landscapes, followed later by grasslands. Many herbivores that radiated in these new landscapes underwent a switch from browsing to grazing associated with increased unguligrade cursoriality and body size, the latter driven by the energetics and constraints of cellulose digestion (fermentation). Carnivores also increased in size and digitigrade, cursorial capacity to occupy a size distribution allowing the capture of prey of the widest range of body sizes. With the emergence of larger, faster carnivores, plantigrade mammals were constrained from evolving to large body sizes and most remained smaller than 1 kg throughout the middle Cenozoic. We find no consistent support for either Cope's Rule or Bergmann's Rule in plantigrade mammals, the largest locomotor guild (n = 1186, 59% of species in the database). Some cold‐specialist plantigrade mammals, such as beavers and marmots, showed dramatic increases in body mass following the Miocene Climate Optimum which may, however, be partially explained by Bergmann's rule. This study reemphasizes the necessity of considering the evolutionary history and resultant form and function of mammalian morphotypes when attempting to understand contemporary mammalian body size distributions.     

Cope's rule and the evolution of body size in Pinnipedimorpha (Mammalia: Carnivora)

Cope's rule describes the evolutionary trend for animal lineages to increase in body size over time. In this study, we tested the validity of Cope's rule for a marine mammal clade, the Pinnipedimorpha, which includes the extinct Desmatophocidae, and extant Phocidae (earless seals), Otariidae (fur seals and sea lions), and Odobenidae (walruses). We tested for the presence of Cope's rule by compiling a large dataset of body size data for extant and fossil pinnipeds and then examined how body size evolved through time. We found that there was a positive relationship between geologic age and body size. However, this trend is the result of differences between early assemblages of small-bodied pinnipeds (Oligocene to early Miocene) and later assemblages (middle Miocene to Pliocene) for which species exhibited greater size diversity. No significant differences were found between the number of increases or decreases in body size within Pinnipedimorpha or within specific pinniped clades. This suggests that the pinniped body size increase was driven by passive diversification into vacant niche space, with the common ancestor of Pinnipedimorpha occurring near the minimum adult body size possible for a marine mammal. Based upon the above results, the evolutionary history of pinnipeds does not follow Cope's rule.     

The extended Price equation quantifies species selection on mammalian body size across the Palaeocene/Eocene Thermal Maximum

Species selection, covariation of species’ traits with their net diversification rates, is an important component of macroevolution. Most studies have relied on indirect evidence for its operation and have not quantified its strength relative to other macroevolutionary forces. We use an extension of the Price equation to quantify the mechanisms of body size macroevolution in mammals from the latest Palaeocene and earliest Eocene of the Bighorn and Clarks Fork Basins of Wyoming. Dwarfing of mammalian taxa across the Palaeocene/Eocene Thermal Maximum (PETM), an intense, brief warming event that occurred at approximately 56 Ma, has been suggested to reflect anagenetic change and the immigration of small bodied-mammals, but might also be attributable to species selection. Using previously reconstructed ancestor–descendant relationships, we partitioned change in mean mammalian body size into three distinct mechanisms: species selection operating on resident mammals, anagenetic change within resident mammalian lineages and change due to immigrants. The remarkable decrease in mean body size across the warming event occurred through anagenetic change and immigration. Species selection also was strong across the PETM but, intriguingly, favoured larger-bodied species, implying some unknown mechanism(s) by which warming events affect macroevolution.     

Predicting woodrat (Neotoma) responses to anthropogenic warming from studies of the palaeomidden record

Aim The influence of anthropogenic climate change on organisms is an area of great scientific concern. Increasingly there is recognition that abrupt climate transitions have occurred over the late Quaternary; studies of these shifts may yield insights into likely biotic responses to contemporary warming. Here, we review research undertaken over the past decade investigating the response of Neotoma (woodrats) body size and distribution to climate change over the late Quaternary (the last 40,000 years). By integrating information from woodrat palaeomiddens, historical museum specimens and field studies of modern populations, we identify potential evolutionary responses to climate change occurring over a variety of temporal and spatial scales. Specifically, we characterize climatic thresholds in the past that led to local species extirpation and/or range alterations rather than in situ adaptation, and apply them to anticipate potential biotic responses to anthropogenic climate change. Location Middens were collected at about 55 sites scattered across the western United States, ranging from about 34 to 46° N and about 104 to 116° W, respectively. Data for modern populations were drawn from studies conducted in Death Valley, California, Missoula, Montana and the Sevilleta LTER site in central New Mexico. Methods We analysed faecal pellets from midden series collected at numerous cave sites across the western United States. From these we estimated body mass using techniques validated in earlier studies. We compared body size fluctuations at different elevations in different regions and integrated these results with studies investigating temperature–body size tradeoffs in modern animals. We also quantify the rapidity of the size changes over the late Quaternary to estimate the evolutionary capacity of woodrats to deal with predicted rates of anthropogenic climate change over the next century. Results We find remarkable similarities across the geographical range to late Quaternary climate change. In the middle of the geographical range woodrats respond in accordance to Bergmann's rule: colder climatic conditions select for larger body size and warmer conditions select for smaller body size. Patterns are more complicated at range boundaries, and local environmental conditions influence the observed response. In general, woodrat body size fluctuates with approximately the same amplitude and frequency as climate; there is a significant and positive correlation between woodrat body size and generalized climate proxies (such as ice core records). Woodrats have achieved evolutionary rates of change equal to or greater than those needed to adapt in situ to anthropogenic climate change. Main conclusions In situ body size evolution is a likely outcome of climate change, and such shifts are part of a normal spectrum of adaptation. Woodrats appear to be subject to ongoing body size selection in response to fluctuating environmental conditions. Allometric considerations suggest that these shifts in body size lead to substantial changes in the physiology, life history and ecology of woodrats, and on their direct and indirect interactions with other organisms in the ecosystem. Our work highlights the importance of a finely resolved and long‐term record in understanding biotic responses to climatic shifts.     

Giant lizards occupied herbivorous mammalian ecospace during the Paleogene greenhouse in Southeast Asia

Mammals dominate modern terrestrial herbivore ecosystems, whereas extant herbivorous reptiles are limited in diversity and body size. The evolution of reptile herbivory and its relationship to mammalian diversification is poorly understood with respect to climate and the roles of predation pressure and competition for food resources. Here, we describe a giant fossil acrodontan lizard recovered with a diverse mammal assemblage from the late middle Eocene Pondaung Formation of Myanmar, which provides a historical test of factors controlling body size in herbivorous squamates. We infer a predominately herbivorous feeding ecology for the new acrodontan based on dental anatomy, phylogenetic relationships and body size. Ranking body masses for Pondaung Formation vertebrates indicates that the lizard occupied a size niche among the larger herbivores and was larger than most carnivorous mammals. Paleotemperature estimates of Pondaung Formation environments based on the body size of the new lizard are approximately 2–5°C higher than modern. These results indicate that competitive exclusion and predation by mammals did not restrict body size evolution in these herbivorous squamates, and elevated temperatures relative to modern climates during the Paleogene greenhouse may have resulted in the evolution of gigantism through elevated poikilothermic metabolic rates and in response to increases in floral productivity.     

Diversity dynamics of Miocene mammals in relation to the history of tectonism and climate

Continental biodiversity gradients result not only from ecological processes, but also from evolutionary and geohistorical processes involving biotic turnover in landscape and climatic history over millions of years. Here, we investigate the evolutionary and historical contributions to the gradient of increasing species richness with topographic complexity. We analysed a dataset of 418 fossil rodent species from western North America spanning 25 to 5 Ma. We compared diversification histories between tectonically active (Intermontane West) and quiescent (Great Plains) regions. Although diversification histories differed between the two regions, species richness, origination rate and extinction rate per million years were not systematically different over the 20 Myr interval. In the tectonically active region, the greatest increase in originations coincided with a Middle Miocene episode of intensified tectonic activity and global warming. During subsequent global cooling, species richness declined in the montane region and increased on the Great Plains. These results suggest that interactions between tectonic activity and climate change stimulate diversification in mammals. The elevational diversity gradient characteristic of modern mammalian faunas was not a persistent feature over geologic time. Rather, the Miocene rodent record suggests that the elevational diversity gradient is a transient feature arising during particular episodes of Earth''s history.     

THE MICRO AND MACRO IN BODY SIZE EVOLUTION

The diversity of body sizes of organisms has traditionally been explained in terms of microevolutionary processes: natural selection owing to differential fitness of individual organisms, or to macroevolutionary processes: species selection owing to the differential proliferation of phylogenetic lineages. Data for terrestrial mammals and birds indicate that even on a logarithmic scale frequency distributions of body mass among species are significantly skewed towards larger sizes. We used simulation models to evaluate the extent to which macro- and microevolutionary processes are sufficient to explain these distributions. Simulations of a purely cladogenetic process with no bias in extinction or speciation rates for different body sizes did not produce skewed log body mass distributions. Simulations that included size-biased extinction rates, especially those that incorporated anagenetic size change within species between speciation and extinction events, regularly produced skewed distributions. We conclude that although cladogenetic processes probably play a significant role in body size evolution, there must also be a significant anagenetic component. The regular variation in the form of mammalian body size distributions among different-sized islands and continents suggests that environmental conditions, operating through both macro- and microevolutionary processes, determine to a large extent the diversification of body sizes within faunas. Macroevolution is not decoupled from microevolution.     

Bird evolution in the Eocene: climate change in Europe and a Danish fossil fauna

The pattern of the evolutionary radiation of modern birds (Neornithes) has been debated for more than 10 years. However, the early fossil record of birds from the Paleogene, in particular, the Lower Eocene, has only recently begun to be used in a phylogenetic context to address the dynamics of this major vertebrate radiation. The Cretaceous-Paleogene (K-P) extinction event dominates our understanding of early modern bird evolution, but climate change throughout the Eocene is known to have also played a major role. The Paleocene and Lower Eocene was a time of avian diversification as a result of favourable global climatic conditions. Deteriorations in climate beginning in the Middle Eocene appear to be responsible for the demise of previously widespread avian lineages like Lithornithiformes and Gastornithidae. Other groups, such as Galliformes display replacement of some lineages by others, probably related to adaptations to a drier climate. Finally, the combination of slowly deteriorating climatic conditions from the Middle Eocene onwards, appears to have slowed the evolutionary rate in Europe, as avian faunas did not differentiate markedly until the Oligocene. Taking biotic factors in tandem with the known Paleogene fossil record of Neornithes has recently begun to illuminate this evolutionary event. Well-preserved fossil taxa are required in combination with ever-improving phylogenetic hypotheses for the inter-relationships of modern birds founded on morphological characters. One key avifauna of this age, synthesised for the first time herein, is the Lower Eocene Fur Formation of Denmark. The Fur birds represent some of the best preserved (often in three dimensions and with soft tissues) known fossil records for major clades of modern birds. Clear phylogenetic assessment of these fossils will prove critical for future calibration of the neornithine evolutionary timescale. Some early diverging clades were clearly present in the Paleocene as evidenced directly by new fossil material alongside the phylogenetically constrained Lower Eocene taxa. A later Oligocene radiation of clades other than Passeriformes is not supported by available fossil data.     

Interspecific geographic range size–body size relationship and the diversification dynamics of Neotropical furnariid birds

Among the earliest macroecological patterns documented, is the range and body size relationship, characterized by a minimum geographic range size imposed by the species’ body size. This boundary for the geographic range size increases linearly with body size and has been proposed to have implications in lineages evolution and conservation. Nevertheless, the macroevolutionary processes involved in the origin of this boundary and its consequences on lineage diversification have been poorly explored. We evaluate the macroevolutionary consequences of the difference (hereafter the distance) between the observed and the minimum range sizes required by the species’ body size, to untangle its role on the diversification of a Neotropical species‐rich bird clade using trait‐dependent diversification models. We show that speciation rate is a positive hump‐shaped function of the distance to the lower boundary. The species with highest and lowest distances to minimum range size had lower speciation rates, while species close to medium distances values had the highest speciation rates. Further, our results suggest that the distance to the minimum range size is a macroevolutionary constraint that affects the diversification process responsible for the origin of this macroecological pattern in a more complex way than previously envisioned.     

The complex drivers of thermal acclimation and breadth in ectotherms

Thermal acclimation capacity, the degree to which organisms can alter their optimal performance temperature and critical thermal limits with changing temperatures, reflects their ability to respond to temperature variability and thus might be important for coping with global climate change. Here, we combine simulation modelling with analysis of published data on thermal acclimation and breadth (range of temperatures over which organisms perform well) to develop a framework for predicting thermal plasticity across taxa, latitudes, body sizes, traits, habitats and methodological factors. Our synthesis includes > 2000 measures of acclimation capacities from > 500 species of ectotherms spanning fungi, invertebrates, and vertebrates from freshwater, marine and terrestrial habitats. We find that body size, latitude, and methodological factors often interact to shape acclimation responses and that acclimation rate scales negatively with body size, contributing to a general negative association between body size and thermal breadth across species. Additionally, we reveal that acclimation capacity increases with body size, increases with latitude (to mid‐latitudinal zones) and seasonality for smaller but not larger organisms, decreases with thermal safety margin (upper lethal temperature minus maximum environmental temperatures), and is regularly underestimated because of experimental artefacts. We then demonstrate that our framework can predict the contribution of acclimation plasticity to the IUCN threat status of amphibians globally, suggesting that phenotypic plasticity is already buffering some species from climate change.     

Climate change and size evolution in an island rodent species: new perspectives on the island rule

As stated by the island rule, small mammals evolve toward gigantism on islands. In addition they are known to evolve faster than their mainland counterparts. Body size in island mammals may also be influenced by geographical climatic gradients or climatic change through time. We tested the relative effects of climate change and isolation on the size of the Japanese rodent Apodemus speciosus and calculated evolutionary rates of body size change since the last glacial maximum (LGM). Currently A. speciosus populations conform both to Bergmann's rule, with an increase in body size with latitude, and to the island rule, with larger body sizes on small islands. We also found that fossil representatives of A. speciosus are larger than their extant relatives. Our estimated evolutionary rates since the LGM show that body size evolution on the smaller islands has been less than half as rapid as on Honshu, the mainland-type large island of Japan. We conclude that island populations exhibit larger body sizes today not because they have evolved toward gigantism, but because their evolution toward a smaller size, due to climate warming since the LGM, has been decelerated by the island effect. These combined results suggest that evolution in Quaternary island small mammals may not have been as fast as expected by the island effect because of the counteracting effect of climate change during this period.     

Geographical range expansion of alien birds and environmental matching

The international wildlife trade is a significant source of introduced alien species, some of which proceed to become invasive and cause negative environmental and economic effects. However, not all introduced aliens establish viable populations, and it is important to identify the factors that determine establishment success. We explore the role of environmental suitability (including anthropogenic influences, climate and habitat types) in the establishment success of alien bird species introduced to Taiwan. Using maximum entropy modelling, we employed a recursive feature elimination and Akaike information criterion (AIC)‐based stepwise model selection approach to assess whether the environmental suitability, native range size, body size, residence time and the numbers of birds for sale in the shops affect variation in the extent of alien bird range size in Taiwan. We show that species with larger native range sizes and larger body sizes tend to have larger alien range sizes in Taiwan. There was no effect of environmental suitability on alien range size in Taiwan, but environmental suitability influenced the establishment success of bird species there.     

Defensive spines are associated with large geographic range but not diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis)

Several prominent evolutionary theories propose mechanisms whereby the evolution of a defensive trait or suite of traits causes significant shifts in species diversification rate and niche evolution. We investigate the role of cuticular spines, a highly variable morphological defensive trait in the hyperdiverse ant genus Polyrhachis, on species diversification and geographic range size. Informed by key innovation theory and the escape-and-radiate hypothesis, we predicted that clades with longer spines would exhibit elevated rates of diversification and larger range sizes compared to clades with shorter spines. To address these predictions, we estimated phylogenetic relationships with a phylogenomic approach utilizing ultraconserved elements and compiled morphological and biogeographic trait databases. In contrast to the first prediction, we found no association between diversification rate and any trait (spine length, body size and range size), with the sole exception of a positive association between range size and diversification in one of three trait-based diversification analyses. However, we recovered a positive phylogenetic correlation between spine length and geographic range size, suggesting that spines promote expanded geographic range. Notably, these results were consistent across analyses using different phylogenetic inference approaches and spine trait measurement schemes. This study provides a rare investigation of the role of a defensive trait on geographic range size, and ultimately supports the hypothesis that defensive spines are a factor in increased range size in Polyrhachis ants. Furthermore, the lack of support for an association between spines and diversification, which contrasts with previous work demonstrating a positive association between spines and diversification rate, is intriguing and warrants further study.     

Shifts in the climate space of temperate cyprinid fishes due to climate change are coupled with altered body sizes and growth rates

Predictions of species responses to climate change often focus on distribution shifts, although responses can also include shifts in body sizes and population demographics. Here, shifts in the distributional ranges (‘climate space’), body sizes (as maximum theoretical body sizes, L∞) and growth rates (as rate at which L∞ is reached, K) were predicted for five fishes of the Cyprinidae family in a temperate region over eight climate change projections. Great Britain was the model area, and the model species were Rutilus rutilus, Leuciscus leuciscus, Squalius cephalus, Gobio gobio and Abramis brama. Ensemble models predicted that the species' climate spaces would shift in all modelled projections, with the most drastic changes occurring under high emissions; all range centroids shifted in a north‐westerly direction. Predicted climate space expanded for R. rutilus and A. brama, contracted for S. cephalus, and for L. leuciscus and G. gobio, expanded under low‐emission scenarios but contracted under high emissions, suggesting the presence of some climate‐distribution thresholds. For R. rutilus, A. brama, S. cephalus and G. gobio, shifts in their climate space were coupled with predicted shifts to significantly smaller maximum body sizes and/or faster growth rates, aligning strongly to aspects of temperature‐body size theory. These predicted shifts in L∞ and K had considerable consequences for size‐at‐age per species, suggesting substantial alterations in population age structures and abundances. Thus, when predicting climate change outcomes for species, outputs that couple shifts in climate space with altered body sizes and growth rates provide considerable insights into the population and community consequences, especially for species that cannot easily track their thermal niches.     

The life history legacy of evolutionary body size change in carnivores

We estimate the body sizes of direct ancestors of extant carnivores, and examine selected aspects of life history as a function not only of species' current size, but also of recent changes in size. Carnivore species that have undergone marked recent evolutionary size change show life history characteristics typically associated with species closer to the ancestral body size. Thus, phyletic giants tend to mature earlier and have larger litters of smaller offspring at shorter intervals than do species of the same body size that are not phyletic giants. Phyletic dwarfs, by contrast, have slower life histories than nondwarf species of the same body size. We discuss two possible mechanisms for the legacy of recent size change: lag (in which life history variables cannot evolve as quickly as body size, leading to species having the 'wrong' life history for their body size) and body size optimization (in which life history and hence body size evolve in response to changes in energy availability); at present, we cannot distinguish between these alternatives. Our finding that recent body size changes help explain residual variation around life history allometries shows that a more dynamic view of character change enables comparative studies to make more precise predictions about species traits in the context of their evolutionary background.