A fifteen-million-year surface- and subsurface-integrated TEX₈₆ temperature record from the eastern equatorial Atlantic

TEX86 is a paleothermometer based on Thaumarcheotal glycerol dialkyl glycerol tetraether (GDGT) lipids and is one of the most frequently used proxies for sea-surface temperature (SST) in warmer-than-present climates. However, the calibration of TEX86 to SST is controversial because its correlation to SST is not significantly stronger than that to depth-integrated surface to subsurface temperatures. Because GDGTs are not exclusively produced in and exported from the surface ocean, sedimentary GDGTs may contain a depth-integrated signal that is sensitive to local subsurface temperature variability, which can only be proved in downcore studies. Here, we present a 15 Myr TEX86 record from ODP Site 959 in the Gulf of Guinea and use additional proxies to elucidate the source of the recorded TEX86 variability. Relatively high GDGT[2/3] ratio values from 13.6 Ma indicate that sedimentary GDGTs were partly sourced from deeper (> 200 m) waters. Moreover, late Pliocene TEX86 variability is highly sensitive to glacial-interglacial cyclicity, as is also recorded by benthic δ18O, while the variability within dinoflagellate assemblages and surface/thermocline temperature records (Uk’37 and Mg/Ca), is not primarily explained by glacial-interglacial cyclicity. Combined, these observations are best explained by TEX86 sensitivity to sub-thermocline temperature variability. We conclude that the TEX86 record represents a depth-integrated signal that incorporates a SST and a deeper component, which is compatible the present-day depth distribution of Thaumarchaeota and with the GDGT[2/3] distribution in core tops. The depth-integrated TEX86 record can potentially be used to infer SST variability, because subsurface temperature variability is generally tightly linked to SST variability. Using a subsurface calibration with peak calibration weight between 100–350 m, we estimate that east equatorial Atlantic SST cooled by ~4.5 °C between the Late Miocene and Pleistocene. On shorter timescales, we use the TEX86 record as an Antarctic Intermediate Water (AAIW) proxy and evaluate climatological leads and lags around the Pliocene M2 glacial (~3.3 Ma). Our record, combined with published information, suggests that the M2 glacial was marked by AAIW cooling during an austral summer insolation minimum, and that decreasing CO2 levels were a feedback, not the initiator, of glacial expansion.

Holocene glacier history of northeastern Cordillera Darwin, southernmost South America (55°S)

In the Cordillera Darwin, southernmost South America, we used 10Be and 14C dating, dendrochronology, and historical observations to reconstruct the glacial history of the Dalla Vedova valley from deglacial time to the present. After deglacial recession into northeastern Darwin and Dalla Vedova, by ~16 ka, evidence indicates a glacial advance at ~13 ka coeval with the Antarctic Cold Reversal. The next robustly dated glacial expansion occurred at 870 ± 60 calendar yr ago (approximately AD 1150), followed by less-extensive dendrochronologically constrained advances from shortly before AD 1836 to the mid-twentieth century. Our record is consistent with most studies within the Cordillera Darwin that show that the Holocene glacial maximum occurred during the last millennium. This pattern contrasts with the extensive early- and mid-Holocene glacier expansions farther north in Patagonia; furthermore, an advance at 870 ± 60 yr ago may suggest out-of-phase glacial advances occurred within the Cordillera Darwin relative to Patagonia. We speculate that a southward shift of westerlies and associated climate regimes toward the southernmost tip of the continent, about 900–800 yr ago, provides a mechanism by which some glaciers advanced in the Cordillera Darwin during what is generally considered a warm and dry period to the north in Patagonia.

Post-glacial expansion dynamics, not refugial isolation, shaped the genetic structure of a migratory bird, the Yellow Warbler (Setophaga petechia)

During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra and permafrost leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated, insular populations that persisted in disjunct regions known as refugia. According to this hypothesis, as ice sheets retreated, species recolonised the continent from these glacial refugia, and the mixing of these lineages is responsible for modern patterns of genetic diversity. However, an alternative hypothesis is that complex genetic patterns could also arise simply from heterogenous post-glacial expansion dynamics, without separate refugia. Both mitochondrial and genomic data from the North American Yellow warbler (Setophaga petechia) shows the presence of an eastern and western clade, a pattern often ascribed to the presence of two refugia. Using a climate-informed spatial genetic modelling (CISGeM) framework, we were able to reconstruct past population sizes, range expansions, and likely recolonisation dynamics of this species, generating spatially and temporally explicit demographic reconstructions. The model captures the empirical genetic structure despite including only a single, large glacial refugium. The contemporary population structure observed in the data was generated during the expansion dynamics after the glaciation and is due to unbalanced rates of northward advance to the east and west linked to the melting of the icesheets. Thus, modern population structure in this species is consistent with expansion dynamics, and refugial isolation is not required to explain it, highlighting the importance of explicitly testing drivers of geographic structure.

Isolation and re-connection: the formation of a ring-shaped speciation continuum in an odorous frog (Odorrana margaretae)

The Green Odorous Frog (Odorrana margaretae) around the Sichuan Basin of western China displays a ring-shaped distributional pattern and possesses multiple replicate contact zones between lineages at various levels of differentiation. To understand its unique speciation history and mechanisms, we obtained 1,540 SNPs from 29 populations and 227 individuals using ddRAD sequencing. Population structure analysis revealed three groups within the species: The West, the North & South, and the East groups. These groups were initially isolated at ~2.03 million years ago, and subsequent post-glacial expansion produced the current ring-shaped distribution around Sichuan Basin with three contact zones. Hybridization in those zones involved lineages with different levels of divergence and produced greatly different outcomes. Both the hybrid zones at southwest (S-W) and southeast (E-NS) of the Basin have extensive admixture and less barrier effect. Consequently, the southern region has the highest genetic diversity and becomes an ‘evolutionary melting pot’. In contrast, the hybrid zone at northwestern corner (N-W), which resembles the overlap zone between two expansion terminals of a ring species, has limited admixture with a narrow geographic cline, suggesting partial reproductive isolation between the northern and western populations. The three hybrid zones likely resemble three time points along a speciation continuum; while both E-NS and S-W hybrid zones are merging, the N-W zone may have passed the ‘tipping point’ and is destined for a complete reproductive isolation over time.

Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds

Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post-glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub-haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence.

Phylogeography of the widespread white-eared hummingbird (Hylocharis leucotis): pre-glacial expansion and genetic differentiation of populations separated by the Isthmus of Tehuantepec

The Pleistocene glacial cycles had a strong influence on the demography and genetic structure of many species, particularly on northern-latitude taxa. Here we studied the phylogeography of the white-eared hummingbird (Hylocharis leucotis), a widely distributed species of the highlands of Mexico and Central America. Analysis of mitochondrial DNA (mtDNA) sequences was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. Analyses of 108 samples from 11 geographic locations revealed population structure and genetic differentiation among populations separated by the Isthmus of Tehuantepec (IT) and the Motagua-Polochic-Jocotán (MPJ) fault barriers. ENM predicted a widespread distribution of suitable habitat for H. leucotis since the Last Inter Glacial (LIG), but this habitat noticeably contracted and fragmented at the IT. Models for historical dispersal corridors based on population genetics data and ENM revealed the existence of corridors among populations west of the IT; however, the connectivity of populations across the IT has changed little since the LIG. The shallow geographic structure on either side of the isthmus and a star-like haplotype network, combined with the long-term persistence of populations across time based on genetic data and potential dispersal routes, support a scenario of divergence with migration and subsequent isolation and differentiation in Chiapas and south of the MPJ fault. Our findings corroborate the profound effects of Pleistocene climatic fluctuations on the evolutionary history of montane taxa but challenge the generality of expanded suitable habitat (pine-oak forests) during glacial cycles.

Late Holocene fluctuations of Stoppani Glacier, southernmost Patagonia

Some lateral moraines contain a rich record of Holocene glacial expansion. Previous workers have used such evidence to document glacial fluctuations in western Canada, Alaska, and the U.S. Pacific Northwest, but similar studies in Patagonia are uncommon. Here we report on the late Holocene behavior of Stoppani Glacier, a 75 km2 glacier sourced in the Cordillera Darwin, southernmost Patagonia. Based on radiocarbon-dated wood and organic material contained in the glacier's northeast lateral moraine, we infer that Stoppani Glacier advanced shortly before 3.8–3.6, at 3.2–2.8, 2.3–2.1, and 0.3–0.2, and possibly sometime before 1.4–1.3 and 0.8–0.7 cal ka BP. These advances culminated at 0.3–0.2 cal ka BP, when the glacier constructed a prominent end moraine, marking its greatest extent of the past 4000 years. Although the timing of several of the advances overlap with the age range of glacial expansion recognized elsewhere in Patagonia, some do not. Asynchronous behavior observed in the glacial record may arise from the type of evidence (e.g., lateral stratigraphy vs. end moraine) used to document glacial fluctuations or variations in climate or glacial response times. A significant difference between the Stoppani record and some other Patagonian records is that the former indicates general expansion of ice over the last 4000 years, whereas the latter indicate a net decrease in extent over that period.

Genetic Structure and Phylogeography of Tuber magnatum Populations

The ectomycorrhizal fungus Tuber magnatum produces the white truffle appreciated worldwide for its unique aroma. With respect to other Tuber spp. of economic interest, T. magnatum presents a narrower geographical range. This species has, in fact, long been considered endemic to Italy. However, over the last few decades several reports have documented the presence of white truffles in different Mediterranean countries and in particular in various areas of south-east Europe. In this study, samples from several Pannonian and Balkan countries such as Hungary, Serbia, Romania, Bulgaria and Greece have been collected and genotyped with microsatellite markers and the data merged with those available for Italian populations. Our objectives were to test whether Italian and south-east European populations are differentiated and to evaluate the genetic diversity of T. magnatum all over its distributional range. We show the genetic structure of T. magnatum populations with the differentiation of four main groups: northern Italy, central-northern Italy, southern Italy and the Balkan/Pannonian region. The present study allowed us to refine the evolutionary history of T. magnatum and track the possible post-glacial expansion route of this species. The assessment of T. magnatum’s genetic structure is not only of scientific relevance, but it is also important for the conservation and market traceability of this prestigious fungus.

Congruence between fine-scale genetic breaks and dispersal potential in an estuarine seaweed across multiple transition zones

Genetic structure in biogeographical transition zones can be shaped by several factors including limited dispersal across barriers, admixture following secondary contact, differential selection, and mating incompatibility. A striking example is found in Northwest France and Northwest Spain, where the estuarine seaweed Fucus ceranoides L. exhibits sharp, regional genetic clustering. This pattern has been related to historical population fragmentation and divergence into distinct glacial refugia, followed by post-glacial expansion and secondary contact. The contemporary persistence of sharp ancient genetic breaks between nearby estuaries has been attributed to prior colonization effects (density barriers) but the effect of oceanographic barriers has not been tested. Here, through a combination of mesoscale sampling (15 consecutive populations) and population genetic data (mtIGS) in NW France, we define regional genetic disjunctions similar to those described in NW Iberia. Most importantly, using high resolution dispersal simulations for Brittany and Iberian populations, we provide evidence for a central role of contemporary hydrodynamics in maintaining genetic breaks across these two major biogeographic transition zones. Our findings further show the importance of a comprehensive understanding of oceanographic regimes in hydrodynamically complex coastal regions to explain the maintenance of sharp genetic breaks along continuously populated coastlines.