The Great American Interchange in birds: a phylogenetic perspective with the genus Trogon

The 'Great American Interchange' (GAI) is recognized as having had a dramatic effect on biodiversity throughout the Neotropics. However, investigation of patterns in Neotropical avian biodiversity has generally been focused on South American taxa in the Amazon Basin, leaving the contribution of Central American taxa under-studied. More rigorous studies of lineages distributed across the entire Neotropics are needed to uncover phylogeographical patterns throughout the area, offering insights into mechanisms that contribute to overall Neotropical biodiversity. Here we use mitochondrial DNA sequence data and intensive geographical sampling from the widespread Neotropical avian genus Trogon to investigate the role of the GAI in shaping its phylogeographical history. Our results show that genetic diversity in Trogon exceeds the perceived biodiversity, and that the GAI resulted in lineage diversification within the genus. Despite greater diversity in South America, a Central American centre of origin with multiple and independent dispersals into South America is indicated. These dispersals were followed by the evolution of divergent lineages associated with the Andes Mountains and other South American geographical features. According to our phylogenetic reconstructions, several species, which were originally defined by morphological characters, are nonmonophyletic. In sum, our results elucidate the evolutionary history of Trogon , reveal patterns obscured by extant biodiversity, and serve as a biogeographical model to consider in future studies.     

Amphibian phylogeography in the Antipodes: Refugia and postglacial colonization explain mitochondrial haplotype distribution in the Patagonian frog Eupsophus calcaratus (Cycloramphidae)

Climatic oscillations, heterogeneity in elevation, topographical position, and isolation time in southwestern Patagonia have been important in promoting diversification of the biota. Geological studies have shown that this region had wide ice-free areas during periods of the last glacial maximum and provided forested refugia for the biota during Pleistocene glaciations. In this study, we sampled the endemic frog Eupsophus calcaratus from 20 localities, covering most of its distribution and including glaciated and non-glaciated regions. We collected DNA sequences for three mitochondrial regions (D-loop, cyt b, 16S), and describe patterns of variation consistent with a history of both the displacement to glacial refugia and recent recolonization to extensively glaciated regions. The inferred demographic history and divergence times of the lineages of E. calcaratus suggest that the Pleistocene had profound effects on the genetic patterns within this taxon in which some populations were able to survive in refugia within colder regions followed by demographic increases but without evidence of significant range expansion. The mtDNA gene tree recovers six major haploclades of E. calcaratus, which we consider diagnostic of species lineages. These results contribute to our understanding of how geological events, predominately glacial oscillations, have influenced current population structure of a broad-ranging, ectothermic vertebrate in the Valdivian Forest region of southern South America.     

Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone

Aim We used inferences of phylogeographical structure and estimates of divergence times for three species of gophersnakes (Colubridae: Pituophis) distributed across the Mexican Transition Zone (MTZ) to evaluate the postulated association of three Neogene geological events (marine seaway inundation of the Isthmus of Tehuantepec, formation of the Transvolcanic Belt across central Mexico, and secondary uplifting of the Sierra Madre Occidental) and of Pleistocene climate change with inter‐ and intraspecific diversification. Location Mexico, Guatemala, and the western United States. Methods We combined range‐wide sampling (67 individuals representing three putative species distributed across northern Middle America and western North America) and phylogenetic analyses of 1637 base pairs of mitochondrial DNA to estimate genealogical relationships and divergence times. The hypothesized concordance of inferred gene trees with geological histories was assessed using topology tests. Results We identified three major lineages of Middle American gophersnakes, and strong phylogeographical structure within each lineage. Gene trees were statistically congruent with hypothesized geological histories for two of the three postulated geological events. Estimated divergence dates and the geographical distribution of genetic variation further support mixed responses to these geological events. Considerable phylogeographical structure appears to have been generated during the Pleistocene. Main conclusions Phylogenetic and phylogeographical structure in gophersnakes distributed across northern Middle America and western North America highlights the influence of both Neogene vicariance events and Pleistocene climate change in shaping genetic diversity in this region. Despite the presence of two major geographical barriers in southern Mexico, extreme geological and environmental heterogeneity in this area may have differentially structured genetic diversity in highland taxa. To the north, co‐distributed taxa may display a more predictable pattern of diversification across the warm desert regions. Future studies should incorporate nuclear data to disentangle inferred lineage boundaries and further elucidate patterns of mitochondrial introgression.     

A tale of North and South America: time and mode of dispersal of the amphitropical genus Munroa (Poaceae,Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping‐stone dispersal and long‐distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 110–125.     

Metabolic Rate and Climatic Fluctuations Shape Continental Wide Pattern of Genetic Divergence and Biodiversity in Fishes

Taxonomically exhaustive and continent wide patterns of genetic divergence within and between species have rarely been described and the underlying evolutionary causes shaping biodiversity distribution remain contentious. Here, we show that geographic patterns of intraspecific and interspecific genetic divergence among nearly all of the North American freshwater fish species (>750 species) support a dual role involving both the late Pliocene-Pleistocene climatic fluctuations and metabolic rate in determining latitudinal gradients of genetic divergence and very likely influencing speciation rates. Results indicate that the recurrent glacial cycles caused global reduction in intraspecific diversity, interspecific genetic divergence, and species richness at higher latitudes. At the opposite, longer geographic isolation, higher metabolic rate increasing substitution rate and possibly the rapid accumulation of genetic incompatibilities, led to an increasing biodiversity towards lower latitudes. This indicates that both intrinsic and extrinsic factors similarly affect micro and macro evolutionary processes shaping global patterns of biodiversity distribution. These results also indicate that factors favouring allopatric speciation are the main drivers underlying the diversification of North American freshwater fishes.     

Comparative phylogeography reveals a shared impact of pleistocene environmental change in shaping genetic diversity within nine Anopheles mosquito species across the Indo-Burma biodiversity hotspot

South-East Asia is one of the world's richest regions in terms of biodiversity. An understanding of the distribution of diversity and the factors shaping it is lacking, yet essential for identifying conservation priorities for the region's highly threatened biodiversity. Here, we take a large-scale comparative approach, combining data from nine forest-associated Anopheles mosquito species and using statistical phylogeographical methods to disentangle the effects of environmental history, species-specific ecology and random coalescent effects. Spatially explicit modelling of Pleistocene demographic history supports a common influence of environmental events in shaping the genetic diversity of all species examined, despite differences in species' mtDNA gene trees. Populations were periodically restricted to allopatric northeastern and northwestern refugia, most likely due to Pleistocene forest fragmentation. Subsequent southwards post-glacial recolonization is supported by a north-south gradient of decreasing genetic diversity. Repeated allopatric fragmentation and recolonization have led to the formation of deeply divergent geographical lineages within four species and a suture zone where these intraspecific lineages meet along the Thai-Myanmar border. A common environmental influence for this divergence was further indicated by strong support for simultaneous divergence within the same four species, dating to approximately 900 thousand years ago (kya). Differences in the geographical structuring of genetic diversity between species are probably the result of varying species' biology. The findings have important implications for conservation planning; if the refugial regions and suture zone identified here are shared by other forest taxa, the unique and high levels of genetic diversity they house will make these areas conservation priorities.     

Phylogeographic Studies Depict the Role of Space and Time Scales of Plant Speciation in a Highly Diverse Neotropical Region

Phylogeographic studies have merged different disciplines to explain speciation processes at both spatial and time scales. Although the number of phylogeographic extant studies has increased almost exponentially, few have been conducted in tropical countries, especially using plants. Plants are interesting models for such studies because their responses to different habitat conditions are reflected directly in the size and distribution of populations, enabling direct tests of alternative demographic scenarios. Here, we review phylogeographic studies using plant species occurring in different vegetation domains within Brazil, which has the greatest number of plant species in the world. Based on a detailed examination of 41 published articles, we synthesized the current knowledge and discussed the main processes driving the high levels of plant diversity within Brazilian domains. General patterns of diversification could be inferred due to the number of species studied, especially in the Cerrado and Atlantic Forest, the most intensively studied domains (34.1% and 17.1% of the studies, respectively). Distinct vegetation types within both biomes were affected differently by the Pleistocene climatic oscillations. Edaphic conditions and geographical barriers (rivers and mountains) have also influenced the phylogeographical patterns of plants species from Amazonia and the Atlantic Forest. Other Brazilian domains, such as the Caatinga, Pantanal, and Pampas, have been studied to a lesser extent and no common phylogeographic pattern across species could be inferred. Issues regarding past connections between distinct domains also remain unclear, including those affecting the two main forest domains in South America. Future research on plant species will fill these information gaps, improving our understanding of the complex diversification processes affecting the South American biota.     

Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia

ABSTRACT: BACKGROUND: The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae). First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods. RESULTS: The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33-42 Ma) origin in North America. Two independent lineages (Battus and Euryades+Parides) reached South America via the GAARlandia connection, and later became extinct in North America. They only began substantive diversification during the Miocene in Amazonia. Macroevolutionary analysis supports the "museum model" of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages. CONCLUSIONS: This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ; (ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii) colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv) Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed the persistence of old lineages and contributed to the steady accumulation of diversity over time with constant net diversification rates, a result that contrasts with previous studies on other South American butterflies.     

Multilocus phylogeography of a widespread savanna–woodland‐adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region

Understanding historical influences of climate and physiographic barriers in shaping patterns of biodiversity remains limited for many regions of the world. For mammals of continental Africa, phylogeographic studies, particularly for West African lineages, implicate both geographic barriers and climate oscillations in shaping small mammal diversity. In contrast, studies for southern African species have revealed conflicting phylogenetic patterns for how mammalian lineages respond to both climate change and geologic events such as river formation, especially during the Pleistocene. However, these studies were often biased by limited geographic sampling or exclusively focused on large‐bodied taxa. We exploited the broad southern African distribution of a savanna–woodland‐adapted African rodent, Gerbilliscus leucogaster (bushveld gerbil) and generated mitochondrial, autosomal and sex chromosome data to quantify regional signatures of climatic and vicariant biogeographic phenomena. Results indicate the most recent common ancestor for all G. leucogaster lineages occurred during the early Pleistocene. We documented six divergent mitochondrial lineages that diverged ~0.270–0.100 mya, each of which was geographically isolated during periods characterized by alterations to the course of the Zambezi River and its tributaries as well as regional ‘megadroughts’. Results demonstrate the presence of a widespread lineage exhibiting demographic expansion ~0.065–0.035 mya, a time that coincides with savanna–woodland expansion across southern Africa. A multilocus autosomal perspective revealed the influence of the Kafue River as a current barrier to gene flow and regions of secondary contact among divergent mitochondrial lineages. Our results demonstrate the importance of both climatic fluctuations and physiographic vicariance in shaping the distribution of southern African biodiversity.     

The impact of early Quaternary climate change on the diversification and population dynamics of a South American cactus species

Aim

Climatic oscillations have been suggested to promote speciation and changes in species distributions, mostly in connection with the Last Glacial Maximum (LGM). However, the LGM is just the most recent of the 20+ glacial‐interglacial periods that characterise the Quaternary. Here, we investigate the role of climatic changes and geomorphological features in shaping the evolution, distribution and population dynamics of the South American cactus Cereus hildmannianus.

Location

South‐eastern South America.

Methods

We built a large fossil‐calibrated phylogeny for cacti (family Cactaceae), comprising 128 species distributed in all subfamilies, using a Bayesian relaxed clock. We used the results to derive a secondary calibration for a population‐level phylogeny in C. hildmannianus. We amplified two plastid (trnQ‐5′rps16 and psbJ‐petA) and one nuclear marker (PhyC) for 24 populations. We estimated population dynamics, ancestral areas, and species distribution models to infer the clade's evolutionary history in time and space.

Results

Our results show a major population divergence of C. hildmannianus at c. 2.60 Ma, which is strikingly coincident with the transition of the Pliocene–Pleistocene and onset of Quaternary glaciations. This was followed by a complex phylogeographic scenario involving population expansions across ecologically diverse regions.

Main conclusions

Contrary to the dominant research focus on the LGM, our study indicates a major impact of the first Quaternary glaciation on the distribution and population divergence of a South American plant species. Further intraspecific events seem related to successive climatic changes and geomorphology, including the development of the coastal plain and its peculiar diversity. We propose that the first Quaternary glaciation acted as a major evolutionary bottleneck, whereby many warm‐adapted lineages succumbed, while those that survived could diversify and better cope with subsequent climatic oscillations.     

An asymmetry in niche conservatism contributes to the latitudinal species diversity gradient in New World vertebrates

The Tropical Niche Conservatism hypothesis is a leading explanation for why biodiversity increases towards the equator. The model suggests that most lineages have tropical origins, with few dispersing into temperate regions. However, biotas are comprised of lineages with differing geographical origins, thus it is unclear whether lineages that originated on different continents will exhibit similar patterns of niche conservatism. Here, we summarised biogeographical patterns of New World vertebrates and compared species diversity patterns between families that originated in North and South America. Overall, families with southern origins exhibit niche conservatism with many lineages restricted to the Neotropics, whereas many northern‐origin families are distributed across the Neotropics and the Nearctic. Consequently, northern lineages have contributed to high tropical biodiversity, but southern lineages have contributed relatively little to temperate biodiversity in North America. The asymmetry in niche conservatism between northern and southern lineages is an important contributor to the biodiversity gradient.     

Plant evolution and endemism in Andean South America: An introduction

Andean South America, including the adjacent lowland environments, can be evaluated in reference to the patterns and processes that characterize plant diversity, evolution, and distribution. Although its ecological complexity is bewildering and the evolutionary and geological history is convoluted and poorly understood, progress can be made by testing the relationship of known processes and paleoevents to patterns of diversification and distribution. Plant diversity patterns can be quantified and mapped in order to permit the study of linkages to environmental parameters and to past speciation and extinction processes. Such studies show the importance of dispersal barriers and long altitudinal gradients for the evolution of Andean plants. Phylogenetic studies allow for the tying of these processes to the timing of connections from the Andes to adjacent tropical forests, grasslands, and deserts, to other highlands in South America, or to other continents. They can also reveal temporal relationships among a variety of plant lineages, allowing for the identification of basal groups, of paleoendemics, and of the recently derived neoendemics. The special places in South America that have high representation of these restricted-range taxa can be better understood as a result. In the Andean context, these are often located in isolated habitat islands, with moisture regimes ranging from arid to perhumid. These patterns allow the development of conservation actions that respond to the presence of special places for plant diversification and of special species that require immediate attention. Further research will include the documentation of patterns at ever-finer spatial resolutions, to better match our biodiversity databases with the topographical and ecological features found in South America. The phylogenetics of plant molecular and morphological characters provide a necessary evolutionary framework that can then be compared to processes identified as important among animal and fungi lineages. For Andean South America, coevolution of plant and animal species is an important source of additional complexity, while trends of evolution to occupy drier and/or higher environments appear in numerous lineages. Anthropogenic influences on these patterns and processes are little understood, but humans have affected and will continue to shape the composition, diversity, and geography of South American biota.     

Range-wide chloroplast and mitochondrial DNA imprints reveal multiple lineages and complex biogeographic history for Douglas-fir

The contemporary genetic structure of species offers key imprints of how organisms responded to past geological and climatic events, which have played a crucial role in shaping the current geographical distribution of north-temperate organisms. In this study, range-wide patterns of genetic variation were examined in Douglas-fir (Pseudotsuga menziesii), a dominant forest tree species distributed from Mexico to British Columbia in western North America. Two organelle DNA markers with contrasting modes of inheritance were genotyped for 613 individuals from 44 populations. Two mitotypes and 42 chlorotypes were recovered in this survey. Both genomes showed significant population subdivision, indicative of limited gene flow through seeds and pollen. Three distinct cpDNA lineages corresponding to the Pacific Coast, the Rocky Mountains, and Mexico were observed. The split time of the two lineages from the Rockies lineage was dated back to 8.5 million years (Ma). The most recent common ancestors of Mexican and coastal populations were estimated at 3.2 and 4.8 Ma, respectively. The northern populations of once glaciated regions were characterized by a high level of genetic diversity, indicating a large zone of contact between ancestral lineages. A possible northern refugium was also inferred. The Mexican lineage, which appeared established by southward migration from the Rockies lineage, was characterized by the lowest genetic diversity but highest population differentiation. These results suggest that the effects of Quaternary climatic oscillations on the population dynamics and genetic diversity of Douglas-fir varied substantially across the latitudinal section. The results emphasize the pressing need for the conservation of Mexican Douglas-fir.     

Biogeographically dynamic genetic structure bridging two continents in the monotypic Central American rodent Ototylomys phyllotis

Central America is an ideal region in which to study patterns of historical divergence and population genetic differentiation, because of its extraordinarily dynamic biogeographical, tectonic, and climatic history. The rodent Ototylomys phyllotis is the only extant species of the genus Ototylomys and is distributed within this region from the Isthmus of Tehuantepec, Mexico, to central Costa Rica, offering an excellent opportunity to study spatial and temporal patterns of population structure of the species and to explain the ecological and evolutionary processes responsible for those patterns. We estimated the genetic diversity and structure within and between populations of O. phyllotis, times of divergence, and migration patterns using mitochondrial DNA and a comprehensive combination of phylogenetic and phylogeographical computational analyses. Our results support monophyly of the genus Ototylomys. We identified three major phylogeographical lineages within O. phyllotis that are linked to its diversification and coincide with the main geological features that shaped Middle America. The origin of the genus was before 3.35 Mya, prior to the Great American Biotic Interchange (GABI), and its initial occurrence was near the centre of its current distribution (Honduras/El Salvador), from which it later spread (3.20–2.84 Mya) following a series of GABI pulses. The species showed an initial northward dispersal to the Chiapas and Guatemala highlands (2.27 Mya) followed by diversification. A later dispersal (1.82 Mya) occurred toward both the south (Nicaragua, Costa Rica) and the north (Belize). The Yucatan peninsula was colonized (0.8 Mya) by individuals from Belize. Extremely high radiation and range expansion occurred throughout the entire range, the highest of which was in the Yucatan peninsula (0.125 Mya). © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 593–610.     

Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography

Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.     

Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas

Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi‐taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional‐scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low‐structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long‐distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene–Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in‐depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.     

Genetic consequences of climatic oscillations in the Quaternary

An appreciation of the scale and frequency of climatic oscillations in the past few million years is modifying our views on how evolution proceeds. Such major events caused extinction and repeated changes in the ranges of those taxa that survived. Their spatial effects depend on latitude and topography, with extensive extinction and recolonization in higher latitudes and altitudinal shifts and complex refugia nearer the tropics. The associated population dynamics varied with life history and geography, and the present genetic constitution of the populations and species carry attenuated signals of these past dynamics. Phylogeographic studies with DNA have burgeoned recently and studies are reviewed from the arctic, temperate and tropical regions, seeking commonalities of cause in the resulting genetic patterns. Arctic species show distinct shallow genetic clades with common geographical boundaries. Thus Beringia is distinct phylogeographically, but its role as a refugial source is complex. Arctic taxa do not show the common genetic pattern of southern richness and northern purity in north-temperate species. Temperate refugial regions in Europe and North America show relatively deep DNA divergence for many taxa, indicating their presence over several Ice Ages, and suggesting a mode of speciation by repeated allopatry. DNA evidence indicates temperate species in Europe had different patterns of postglacial colonization across the same area and different ones in previous oscillations, whereas the northwest region of North America was colonized from the north, east and south. Tropical montane regions contain deeply diverged lineages, often in a relatively small geographical area, suggesting their survival there from the Pliocene. Our poor understanding of refugial biodiversity would benefit from further combined fossil and genetic studies.     

Climatic niche conservatism and ecological opportunity in the explosive radiation of arvicoline rodents (Arvicolinae,Cricetidae)

Climatic niche conservatism shapes patterns of diversity in many taxonomic groups, while ecological opportunity (EO) can trigger rapid speciation that is less constrained by the amount of time a lineage has occupied a given habitat. These two processes are well studied, but limited research has considered their joint and relative roles in shaping diversity patterns. We characterized climatic and biogeographic variables for 102 species of arvicoline rodents (Arvicolinae, Cricetidae), testing the effects of climatic niche conservatism and EO on arvicoline diversification as lineages transitioned between biogeographic regions. We found that the amount of time a lineage has occupied a precipitation niche is positively correlated with diversity along a precipitation gradient, suggesting climatic niche conservatism. In contrast, shift in diversification rate explained diversity patterns along a temperature gradient. Our results suggest that an indirect relationship exists between temperature and diversification that is associated with EO as arvicoline rodents colonized warm Palearctic environments. Climatic niche conservatism alone did not fully explain diversity patterns under density‐dependence, highlighting the additional importance of EO‐related processes in promoting the explosive radiation in arvicoline rodents and shaping diversity pattern among biogeographic regions and along climatic gradients.     

The Phylogeographic History of the New World Screwworm Fly,Inferred by Approximate Bayesian Computation Analysis

Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests.     

Multiple cryptic species with divergent substrate affinities in the Serpula himantioides species complex

Serpula himantioides is a widespread saprotrophic morphospecies mainly colonising coniferous wood in nature, but it appears frequently in buildings as well. From an earlier study, it is known that at least three divergent lineages occur within the S. himantioides species complex. In this study, a broader sample of S. himantioides isolates has been analysed by multi-locus sequencing, including new isolates from Asia, North and South America. Altogether five phylogenetical species (PS1-5) were detected, all recognised across independent gene phylogenies. A new southern South American phylogenetic species (PS1) was found, representing an early diverging lineage within the S. himantioides species complex. The two closely related PS2 and PS3 lineages included isolates from North America only, and PS4 was also dominated by North American isolates. Most of the investigated isolates (76%) clustered into PS5, a lineage that has been found on most continents, including North America. Overall, little phylogeographical structure was found in PS5, indicating frequent and recent long-distance dispersal events within this widespread lineage. Our analyses indicate that South and North America are the centres of divergence for the S.?himantioides species complex. Some of the lineages seem adapted to various substrates, but PS5 is able to decay a wide array of angiosperms and gymnosperms, which may have facilitated the spread of this lineage throughout the world.