Glacial cycles as an allopatric speciation pump in north‐eastern American freshwater fishes

Allopatric speciation may be the principal mechanism generating new species. Yet, it remains difficult to judge the generality of this process because few studies have provided evidence that geographic isolation has triggered the development of reproductive isolation over multiple species of a regional fauna. Here, we first combine results from new empirical data sets (7 taxa) and published literature (9 taxa) to show that the eastern Great Lakes drainage represents a multispecies suture zone for glacial lineages of freshwater fishes with variable levels of genetic divergence. Second, we performed amplified fragment length polymorphism analyses among four pairs of lineages. Results indicate that lineages with relatively deep levels of mtDNA 5′ COI (barcode) sequence divergence (>2%) developed strong reproductive barriers, while lineages with lower levels of divergence show weaker reproductive isolation when found in sympatry. This suggests that a threshold of 2% sequence divergence at mtDNA could be used as a first step to flag cryptic species in North American freshwater fishes. By describing different levels of divergence and reproductive isolation in different co‐occurring fishes, we offer strong evidence that allopatric speciation has contributed significantly to the diversification of north‐eastern American freshwater fishes and confirm that Pleistocene glacial cycles can be viewed as a ‘speciation pump’ that played a predominant role in generating biodiversity.     

When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses

The Polydnaviridae (PDV), including the Bracovirus (BV) and Ichnovirus genera, originated from the integration of unrelated viruses in the genomes of two parasitoid wasp lineages, in a remarkable example of convergent evolution. Functionally active PDVs represent the most compelling evolutionary success among endogenous viral elements (EVEs). BV evolved from the domestication by braconid wasps of a nudivirus 100 Ma. The nudivirus genome has become an EVE involved in BV particle production but is not encapsidated. Instead, BV genomes have co-opted virulence genes, used by the wasps to control the immunity and development of their hosts. Gene transfers and duplications have shaped BV genomes, now encoding hundreds of genes. Phylogenomic studies suggest that BVs contribute largely to wasp diversification and adaptation to their hosts. A genome evolution model explains how multidirectional wasp adaptation to different host species could have fostered PDV genome extension. Integrative studies linking ecological data on the wasp to genomic analyses should provide new insights into the adaptive role of particular BV genes. Forthcoming genomic advances should also indicate if the associations between endoparasitoid wasps and symbiotic viruses evolved because of their particularly intimate interactions with their hosts, or if similar domesticated EVEs could be uncovered in other parasites.     

The DroughtBox: A new tool for phenotyping residual branch conductance and its temperature dependence during drought

Xylem hydraulic failure is a major driver of tree death during drought. However, to better understand mortality risk in trees, especially during hot-drought events, more information is required on both rates of residual water-loss from small branches (g_res) after stomatal closure, as well as the phase transition temperature (T_p), beyond which g_res significantly increases. Here, we describe and test a novel low-cost tool, the DroughtBox, for phenotyping g_res and T_p across species. The system consists of a programmable climatically controlled chamber in which branches dehydrate and changes in the mass recorded. Test measurements show that the DroughtBox maintains stable temperature and relative humidity across a range of set points, a prerequisite for getting accurate g_res and T_p values. Among a study group of four conifer and one angiosperm species, we observed a range of g_res (0.44–1.64 mmol H₂O m⁻² s⁻¹) and T_p (39.4–43.8°C) values. Furthermore, the measured time to hydraulic failure varied between two conifers species and was shortened in both species following a heatwave event. The DroughtBox is a reliable and customizable tool for phenotyping g_res and T_p, as well as for testing models of time to hydraulic failure that will improve our ability to assess climate change impacts on plants.     

Quantifying spatial and temporal variation of North Pacific fin whale (Balaenoptera physalus) acoustic behavior

In order to help develop hypotheses of connectivity among North Pacific fin whales, we examine recordings from 10 regions collected in the spring and fall. We develop a Random Forest model to classify fin whale note types that avoids manual note classification errors. We also present a method that objectively quantifies the note and pattern composition of recordings. We find that fin whale recordings near Hawaii have distinctive patterns, similar to those found in other regions in the central North Pacific, suggesting potential migration pathways. Our results are consistent with previous studies that suggest there may be two different populations utilizing the Chukchi Sea and central Aleutians in the fall and mix to some degree in the southern Bering Sea. Conversely, we found little difference between spring and fall recordings in the eastern Gulf of Alaska, suggesting some residency of whales in this region. This is likely due to fine scale similarities of calls among the inshore regions of British Columbia, while offshore areas are being utilized by whales traveling from various distant areas. This study shows how our novel approach to characterize recordings is an objective and informative way to standardize spatial and temporal comparisons of fin whale recordings.     

Genomic footprints of a biological invasion: Introduction from Asia and dispersal in Europe of the topmouth gudgeon (Pseudorasbora parva)

Facilitated by the intensification of global trading, the introduction and dispersal of species to areas in which they are historically non‐native is nowadays common. From an evolutionary standpoint, invasions are paradoxical: not only non‐native environments could be different from native ones for which introduced individuals would be ill‐adapted, but also small founding population size should be associated with reduced adaptive potential. As such, biological invasions are considered valuable real‐time evolutionary experiments. Here, we investigated the population structure and adaptive potential of the highly invasive topmouth gudgeon (Pseudorasbora parva) across Europe and East Asia. We RAD‐sequenced 301 specimens from sixteen populations and three distinct within‐catchment invaded regions as well as two locations in the native range. With 13,785 single nucleotide polymorphisms, we provide conclusive evidence for a genome‐wide signature of two distinct invasion events, in Slovakia and Turkey, each originating from a specific area in the native range. A third invaded area, in France, appears to be the result of dispersal within the invasive range. Few loci showed signs of selection, the vast majority of which being identified in the Slovakian region. Functional annotation suggests that faster early stage development, resistance to pollution and immunocompetence contribute to the invasion success of the local habitats. By showing that populations in the invasive range have different evolutionary histories, our study reinforces the idea that populations, rather than species, are the units to consider in invasion biology.     

Convergent morphological responses to loss of flight in rails (Aves: Rallidae)

The physiological demands of flight exert strong selection pressure on avian morphology and so it is to be expected that the evolutionary loss of flight capacity would involve profound changes in traits. Here, we investigate morphological consequences of flightlessness in a bird family where the condition has evolved repeatedly. The Rallidae include more than 130 recognized species of which over 30 are flightless. Morphological and molecular phylogenetic data were used here to compare species with and without the ability to fly in order to determine major phenotypic effects of the transition from flighted to flightless. We find statistical support for similar morphological response among unrelated flightless lineages, characterized by a shift in energy allocation from the forelimbs to the hindlimbs. Indeed, flightless birds exhibit smaller sterna and wings than flighted taxa in the same family along with wider pelves and more robust femora. Phylogenetic signal tests demonstrate that those differences are independent of phylogeny and instead demonstrate convergent morphological adaptation associated with a walking ecology. We found too that morphological variation was greater among flightless rails than flighted ones, suggesting that relaxation of physiological demands during the transition to flightlessness frees morphological traits to evolve in response to more varied ecological opportunities.     

Maternal effects and urbanization: Variation of yolk androgens and immunoglobulin in city and forest blackbirds

Wildlife inhabiting urban environments exhibit drastic changes in morphology, physiology, and behavior. It has often been argued that these phenotypic responses could be the result of micro‐evolutionary changes following the urbanization process. However, other mechanisms such as phenotypic plasticity, maternal effects, and developmental plasticity could be involved as well. To address maternal effects as potential mechanisms, we compared maternal hormone and antibody concentrations in eggs between city and forest populations of European blackbirds (Turdus merula), a widely distributed species for which previous research demonstrated differences in behavioral and physiological traits. We measured egg and yolk mass, yolk concentrations of androgens (androstenedione [A₄], testosterone [T], 5α‐dihydrotestosterone [5α‐DHT], and immunoglobulins [IgY]) and related them to population, clutch size, laying order, embryo sex, and progress of breeding season. We show (a) earlier onset of laying in the city than forest population, but similar egg and clutch size; (b) higher overall yolk androgen concentrations in the forest than the city population (sex‐dependent for T); (c) greater among‐female variation of yolk T and 5α‐DHT concentrations in the forest than city population, but similar within‐clutch variation; (d) similar IgY concentrations with a seasonal decline in both populations; and (e) population‐specific positive (city) or negative (forest) association of yolk A₄ and T with IgY concentrations. Our results are consistent with the hypotheses that hormone‐mediated maternal effects contribute to differences in behavioral and physiological traits between city and forest individuals and that yolk androgen and immunoglobulin levels can exhibit population‐specific relationships rather than trade‐off against each other.     

Unsustainable anthropogenic mortality disrupts natal dispersal and promotes inbreeding in leopards

Anthropogenic mortality of wildlife is typically inferred from measures of the absolute decline in population numbers. However, increasing evidence suggests that indirect demographic effects including changes to the age, sex, and social structure of populations, as well as the behavior of survivors, can profoundly impact population health and viability. Specifically, anthropogenic mortality of wildlife (especially when unsustainable) and fragmentation of the spatial distribution of individuals (home‐ranges) could disrupt natal dispersal mechanisms, with long‐term consequences to genetic structure, by compromising outbreeding behavior and gene flow. We investigate this threat in African leopards (Panthera pardus pardus), a polygynous felid with male‐biased natal dispersal. Using a combination of spatial (home‐range) and genetic (21 polymorphic microsatellites) data from 142 adult leopards, we contrast the structure of two South African populations with markedly different histories of anthropogenically linked mortality. Home‐range overlap, parentage assignment, and spatio‐genetic autocorrelation together show that historical exploitation of leopards in a recovering protected area has disrupted and reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry, with sons establishing territories closer to their mothers and sisters. The resultant kin‐clustering in males of this historically exploited population is comparable to that of females in a well‐protected reserve and has ultimately led to localized inbreeding. Our findings demonstrate novel evidence directly linking unsustainable anthropogenic mortality to inbreeding through disrupted dispersal in a large, solitary felid and expose the genetic consequences underlying this behavioral change. We therefore emphasize the importance of managing and mitigating the effects of unsustainable exploitation on local populations and increasing habitat fragmentation between contiguous protected areas by promoting in situ recovery and providing corridors of suitable habitat that maintain genetic connectivity.     

The proteome of cytosolic lipid droplets isolated from differentiated Caco-2/TC7 enterocytes reveals cell-specific characteristics

Background information. Intestinal absorption of alimentary lipids is a complex process ensured by enterocytes and leading to TRL [TAG (triacylglycerol)‐rich lipoprotein] assembly and secretion. The accumulation of circulating intestine‐derived TRL is associated with atherosclerosis, stressing the importance of the control of postprandial hypertriglyceridaemia. During the postprandial period, TAGs are also transiently stored as CLDs (cytosolic lipid droplets) in enterocytes. As a first step for determining whether CLDs could play a role in the control of enterocyte TRL secretion, we analysed the protein endowment of CLDs isolated by sucrose‐gradient centrifugation from differentiated Caco‐2/TC7 enterocytes, the only human model able to secrete TRL in culture and to store transiently TAGs as CLDs when supplied with lipids. Cells were analysed after a 24 h incubation with lipid micelles and thus in a state of CLD‐associated TAG mobilization. Results. Among the 105 proteins identified in the CLD fraction by LC‐MS/MS (liquid chromatography coupled with tandem MS), 27 were directly involved in lipid metabolism pathways potentially relevant to enterocyte‐specific functions. The transient feature of CLDs was consistent with the presence of proteins necessary for fatty acid activation (acyl‐CoA synthetases) and for TAG hydrolysis. In differentiated Caco‐2/TC7 enterocytes, we identified for the first time LPCAT2 (lysophosphatidylcholine acyltransferase 2), involved in PC (phosphatidylcholine) synthesis, and 3BHS1 (3‐β‐hydroxysteroid dehydrogenase 1), involved in steroid metabolism, and confirmed their partial CLD localization by immunofluorescence. In enterocytes, LPCAT2 may provide an economical source of PC, necessary for membrane synthesis and lipoprotein assembly, from the lysoPC present in the intestinal lumen. We also identified proteins involved in lipoprotein metabolism, such as ApoA‐IV (apolipoprotein A‐IV), which is specifically expressed by enterocytes and has been proposed to play many functions in vivo, including the formation of lipoproteins and the control of their size. The association of ApoA‐IV with CLD was confirmed by confocal and immunoelectron microscopy and validated in vivo in the jejunum of mice fed with a high‐fat diet. Conclusions. We report for the first time the protein endowment of Caco‐2/TC7 enterocyte CLDs. Our results suggest that their formation and mobilization may participate in the control of enterocyte TRL secretion in a cell‐specific manner.