Pleistocene Climatic Oscillations Research Articles

Climatic variability in the Armenian Highlands as the backdrop to hominin population dynamics 50–25 ka

The impact of Late Pleistocene climatic oscillations, volcanism and the diverse terrain of the Armenian Highlands affected hominin population dynamics and movements through the region. To test different scenarios for the period 50–25 ka regarding expansion, adaptive response, intra-population interactions and extinction, we need local on-site paleoclimatic data found in association with hominin occupations. However, this approach has been hampered by the dearth and highly uneven spatiotemporal recovery of paleoclimatic data from prehistoric sites across the region. In this study, we analyze multiple assemblages of fossil micromammals from the Late Middle Paleolithic (LMP) Lusakert-1 rockshelter (two fossil-yielding strata; <55 ka) and Early Upper Paleolithic (EUP) Aghitu-3 Cave (four fossil-yielding strata; ∼39–24 ka) using geometric morphometric-aided taxonomy, to quantify the representation of different species among the abundant and diverse arvicoline genera (Microtus and Chionomys; mean = 58% of assemblages). We combined this approach with quantitative species-level paleoclimatic reconstructions (Bioclimatic Model; 14 rodent taxa) to determine changes in habitat composition as well as temperature and precipitation shifts during the Late Middle–Early Upper Paleolithic. Taphonomic analysis was conducted to establish isotaphonomy among the assemblages. The analysis shows higher than present-day absolute temperatures for the series of occupations at both Lusakert-1 and Aghitu-3, making it unlikely that hominin activity at the sites coincided with extreme cold-climate phases. A multivariate comparison of the taxonomic abundances (genus level) across a wider sample of regional Middle Paleolithic (MP) and Upper Paleolithic (UP) cave sites (Hovk-1, Kudaro-1, Mezmaiskaya, Satsurblia and Dzudzuana) indicates the possibility of cold-period occupation at only two of the sites, Mezmaiskaya Layers 3 and 2 and Kudaro-1 Layer 3. We surmise that the manufacturers of LMP lithic industries in the Caucasus were well adapted to these challenging environments, thus undermining arguments that rapid climate change through the LMP/EUP period could alone have determined the course of population dynamics in this region.

The phylogenetic relationship and demographic history of rhesus macaques (Macaca mulatta) in subtropical and temperate regions, China.

Pleistocene climatic oscillations exerted significant influences on the genetic structure and demography of rhesus macaque (Macaca mulatta) in eastern China. However, the evolutionary history of rhesus macaques in subtropical and temperate China remained unclear and/or controversial. Herein, we analyzed the autosomes, mitochondrial genomes, and Y-chromosomes from 84 individuals of Chinese rhesus macaque. The results revealed that (1) all individuals were clustered into pan-west and pan-east genetic groups, which exhibited Shaanxi Province as the northernmost region of western dispersal route of rhesus macaques in China; (2) in subtropical and temperate China, rhesus macaques were divided into four lineages (TH, DB, HS, and QL), and their divergence times corresponded to the Penultimate Glaciation (300-130 kya) and Last Glaciation (70-10 kya), respectively; (3) the individuals from Mt. Taihangshan (TH) are closely related to individuals from Mt. Dabashan (DB) in the autosomal tree, rather than individuals from Mt. Huangshan (HS) as indicated by the mitogenome tree, which supports the hypothesis that the ancestral rhesus macaques radiated into Mt. Taihangshan from Mt. Huangshan via Mt. Dabashan; and (4) the demographic scenario of the four lineages showed the ancestral rhesus macaques bottleneck and expansion corresponding to the suitable habitat reduction and expansion, which confirmed they had experienced northward recolonization and southward retreat events from Mt. Huangshan area via Northern China Plain to Northernmost China along with Pleistocene glacial cycles. This study provides a new insight into understanding how Pleistocene glaciation has influenced faunal diversity in subtropical and temperate China, especially for those exhibiting differential patterns of sex dispersal.

Population structure and microscale morphological differentiation in a freshwater snail from the Chilean Altiplano

BackgroundThe diversity and population genetic structure of many species have been shaped by historical and contemporary climatic changes. For the species of the South American Altiplano, the historical climatic changes are mainly related to the wet events of great magnitude and regional influence that occurred during the Pleistocene climatic oscillations (PCOs). In contrast, contemporary climate changes are associated with events of lesser magnitude and local influence related to intensifications of the South American Summer Monsoon (SASM). Although multiple studies have analyzed the effect of PCOs on the genetic patterns of highland aquatic species, little is known about the impact of contemporary climate changes in recent evolutionary history. Therefore, in this study, we investigated the change in population structure and connectivity using nuclear and mitochondrial markers throughout the distribution range of Heleobia ascotanensis, a freshwater Cochliopidae endemic to the Ascotán Saltpan. In addition, using geometric morphometric analyses, we evaluated the concomitance of genetic divergence and morphological differentiation.ResultsThe mitochondrial sequence analysis results revealed the presence of highly divergent co-distributed and geographically nested haplotypes. This pattern reflects an extension in the distribution of groups that previously would have differentiated allopatrically. These changes in distribution would have covered the entire saltpan and would be associated with the large-scale wet events of the PCOs. On the other hand, the microsatellite results defined five spatially isolated populations, separated primarily by geographic barriers. Contemporary gene flow analyses suggest that post-PCO, climatic events that would have connected all populations did not occur. The morphometric analyses results indicate that there is significant morphological differentiation in the populations that are more isolated and that present the greatest genetic divergence.ConclusionsThe contemporary population structure and morphological variation of H. ascotanensis mainly reflect the post-PCO climatic influence. Although both markers exhibit high genetic structuring, the microsatellite and morphology results show the preponderant influence of fragmentation in recent evolutionary history. The contemporary genetic pattern shows that in species that have limited dispersal capabilities, genetic discontinuities can appear rapidly, erasing signs of historical connectivity.

Pleistocene climatic oscillations influenced the emergence of geographically widespread and restricted genetic lineages in an Andean grasshopper species group

Abstract The grasshopper Trimerotropis pallidipennis species complex is distributed across arid and semi-arid environments from North to South America, reaching high altitudes along the Andes Mountain range. Currently, there are four valid species of Trimerotropis in South America. However, some species were found to comprise several genetic lineages. Here, we describe the genetic structure, lineage diversification, and environmental requirements within the Trimerotropis species complex in South America based on sequences from the mitochondrial COI gene, 4048 single nucleotide polymorphisms, and ecological niche modelling. The analyses revealed the existence of at least five lineages: two with a restricted geographical distribution and three with a very wide one. The results provide evidence that glacial cycles promoted not only the presence of refuge areas but also the isolation of widely distributed lineages on the eastern and western sides of the southern Andes, potentially driving the emergence of the Trimerotropis sp. lineage, which can tolerate more temperate habitats. Our results provide evidence for the effects of Pleistocene climatic changes on the diversification history of a South American grasshopper species complex.

Phylogeography and Ecological Niche Modeling of the Alashan Pit Viper (Gloydius cognatus; Reptilia, Viperidae) in Northwest China and Adjacent Areas

The joint impacts of historical geological events and Quaternary climatic oscillations in Northwest China on species evolution have been examined extensively in plant under a phylogeographic perspective. However, animal phylogeographic analyses in this region are still limited. The Alashan pit viper, Gloydius cognatus, occurs primarily in arid Northwest China and adjacent areas. Based on variation at two mtDNA genes (ND4 and Cytb) in 27 individuals representing 24 populations, the spatial genetic structure and demographic history of G. cognatus were examined across its geographic range. Phylogenetic analyses revealed two well-supported allopatric clades (each with two distinct subclades/lineages), distributed across the southern (Qaidam Basin, Lanzhou Basin, and Zoige Basin [S1]; Loess Plateau [S2]) and northern (Ily Basin [N1]; Junggar Basin and Mongolian Plateau [N2]) regions. AMOVA analysis demonstrated that over 76% of the observed genetic variation was related to these lineage splits, indicating substantial genetic differentiation among the four lineages. A strong pattern of isolation-by-distance across the sampling populations suggested that geographic distance principally shaped the genetic structure. The four lineages diverged by 0.9–2.2% for the concatenated data, which were estimated to have coalesced ~1.17 million years ago (Mya), suggesting that the expansions of the Badain Jaran, Tengger, and Mu Us deserts during the Xixiabangma glaciation likely interrupted gene flow and triggered the observed divergence in the southern and northern regions. Subsequently, the early Pleistocene integration of the Yellow River and associated deserts expansion promoted the differentiation of S1 and S2 lineages (~0.9 Mya). Both mitochondrial evidence and ecological niche modeling (ENM) reject the signature of demographic and range contractions during the LGM for G. cognatus. In addition, ENM predicts that the suitable habitat of G. cognatus will contract in the future. As such, the conservation and management of ESUs should be a priority. Our findings provide the first insights on the lineage diversification and population dynamics of the Alashan pit viper in relation to geological history and Pleistocene climatic oscillations in arid Northwest China.

Range wide genetic differentiation in the bull kelp Nereocystis luetkeana with a seascape genetic focus on the Salish Sea

IntroductionIn temperate regions, one of the most critical determinants of present range-wide genetic diversity was the Pleistocene climate oscillations, the most recent one created by the last glacial maximum (LGM). This study aimed to describe N. luetkeana genetic structure across its entire range (Alaska to California) and test different models of population connectivity within the Salish Sea. This region was colonized after the LGM and has been under increased disturbance in recent decades.MethodsWe utilized microsatellite markers to study N. luetkeana genetic diversity at 53 sites across its range. Using higher sampling density in the Salish Sea, we employed a seascape genetics approach and tested isolation by hydrodynamic transport and environment models.ResultsAt the species distribution scale, we found four main groups of genetic co-ancestry, Alaska; Washington with Vancouver Island’s outer coast and Juan de Fuca Strait; Washington’s inner Salish Sea; and Oregon with California. The highest allelic richness (AR) levels were found in California, near the trailing range edge, although AR was also high in Alaska. The inner Salish Sea region had the poorest diversity across the species distribution. Nevertheless, a pattern of isolation by hydrodynamic transport and environment was supported in this region.DiscussionThe levels of allelic, private allele richness and genetic differentiation suggest that during the LGM, bull kelp had both northern and southern glacial refugia in the Prince of Wales Island-Haida Gwaii region and Central California, respectively. Genetic diversity in Northern California sites seems resilient to recent disturbances, whereas the low levels of genetic diversity in the inner Salish Sea are concerning.

Phylogenetics and Population Genetics of the Petrolisthes lamarckii-P. haswelli Complex in China: Old Lineage and New Species.

Petrolisthes lamarckii (Leach, 1821) and P. haswelli Miers, 1884 are a pair of sister species of porcelain crabs, both of which are common in the intertidal zone of southern China, typically found under rocks and in the crevices of coral reefs. However, the distribution, genetic relationship and diversity of the two species in China have not been rigorously studied. Meanwhile, P. lamarckii is considered as a complex of cryptic species due to their diverse morphological features. In this study, we identified 127 specimens of the P. lamarckii-P. haswelli complex (LH complex) and recognised a new species through morphological and molecular analysis. Furthermore, we constructed a time-calibrated phylogeny of the LH complex using three mitochondrial and two nuclear genes from all three species, finding that the divergence of the LH complex can be traced back to the Miocene epoch, and that the genetic diversity increased during the Mid-Pleistocene transition period. Glacial refugia formed during the Pleistocene climatic oscillations has been regarded as one of the contributing factors to the diversification of marine organisms in the north-western Pacific. Petrolisthes haswelli demonstrates a wide distribution along the southern coast of China, while other lineages display more restricted distributions. The research on the demographic history and gene flow of P. haswelli revealed that the Chinese coastal populations experienced an expansion event approximately 12.5 thousand years ago (Kya) and the asymmetrical gene flows were observed between the two sides of the Taiwan Strait and Qiongzhou Strait, respectively, which is likely influenced by the restriction of ocean currents.

Multilocus phylogeny and morphological analyses illuminate overlooked diversity of Soriculus (Mammalia: Eulipotyphla: Soricidae), with descriptions of two new endemic species from the eastern Himalayas

Abstract The genus Soriculus is currently recognized as monotypic, containing only one species, Soriculus nigrescens, which is distributed mainly in the Himalayas and the southern Hengduan Mountains. The taxonomy of Soriculus is ambiguous due to insufficient taxonomic sampling. We conducted extensive surveys of Soriculus across the Himalayas and Hengduan Mountains. We sequenced two mitochondrial and three nuclear genes, and the complete mitochondrial genomes of several selected specimens to infer the phylogenetic relationships of Soriculus and also analysed their morphological and morphometric variations. Our results indicate monophyly of Soriculus, and the diversity of the genus is greatly underestimated. We described two new species, Soriculus nivatus sp. nov. and Soriculus medogensis sp. nov., and elevated S. minor as a distinct species. Additionally, we found another putative new species of Soriculus in Medog County; however, we did not formally describe it because only one specimen was collected. Divergence time estimates suggest that the global cooling and desiccating events around the Miocene/Pliocene and Pliocene/Pleistocene boundaries and the Pleistocene climatic oscillations may have played major roles in the diversification of Soriculus. Our results highlight the overlooked diversity of small mammals in the eastern Himalayas, which warrants further surveys and taxonomic studies.

Demographic processes, refugia and dispersal routes during the Pleistocene in a sigmodontine rodent assemblage from the South American Pampas

Abstract The Pampas of South America represents one of the most extended subtropical–temperate grasslands in the world. This ecoregion was influenced by Pleistocene climate oscillations. The sigmodontine rodent assemblage inhabiting this region is a good model system to analyse the impact of these climate changes on evolutionary histories. We performed a comparative phylogeographical study on seven species to evaluate the concordance of phylogeographical patterns among them, to assess if they experienced congruent and synchronous demographic changes, and posit putative centres of origin and dispersal routes. Four species (Calomys musculinus, Oligoryzomys flavescens, Oxymycterus nasutus and Oligoryzomys nigripes) showed evidence of demographic expansion. In the first three, population increases started during Marine Isotope Stage 5 (MIS 5) while in Ol. nigripes, the rise started during MIS 7; this rise would have continued to the present in all cases. Necromys lasiurus, Scapteromys tumidus and Scapteromys aquaticus did not show a pattern of expansion. Four centres of origin were identified; in general, populations sharing the same putative refugium followed common dispersal routes. Our results indicate that the Pampas offered relatively stable habitats over time, mainly in areas associated with watercourses or coastlines, suggesting that recent Pleistocene climate oscillations have had a moderate impact on this ecoregion compared to other regions of South America.

Climatic adaptation explains responses to Pleistocene oscillations and diversification in European vipers

AbstractAimAllopatric speciation is the primary mode of diversification in the Mediterranean Basin. However, the contribution of climatic adaptation during this process is contradictory. In this work, we investigate the eco‐evolutionary processes that drove diversification in this region, using European vipers as a case study. We describe the climatic requirements of different lineages to compare their responses to the Pleistocene climatic oscillations and tackle the evolutionary mechanisms underlying their diversification.LocationEurasia and North Africa.TaxonEuropean vipers (genus Vipera).MethodsWe used ecological niche modelling (ENM) to identify the climatic requirements of 24 Vipera lineages and infer past range dynamics associated with their diversification during the Pleistocene. To test whether climatic niches varied across lineages, we calculated the phylogenetic signal of different climatic variables and examined the relationship with phylogenetic relatedness. To investigate climatic niche evolution and test for phylogenetic niche conservatism (PNC), we quantified pairwise niche overlap in sister phylogenetic units under a 3D hypervolume approach.ResultsENM identified temperature annual range, precipitation of wettest month and precipitation of driest quarter as the most important climatic variables related to the distribution of most lineages, validating Pelias clade as cold‐adapted, and Vipera 1 and Vipera 2 as warm‐adapted clades. Projections to past conditions varied among clades, with Pelias and Vipera 1 having more similar responses, while Vipera 2 exhibited greater variability. We found significant phylogenetic signal in one temperature‐related and two humidity‐related climatic variables and detected high complexity in ecological niche evolution across the phylogeny, both rejecting the hypothesis of PNC.Main ConclusionsClimatic adaptation played a significant role in driving diversification among European vipers. Cold‐adapted and warm‐adapted lineages presented similar climatic requirements and remarkable responses to Pleistocene stages, resulting in an intricate pattern of niche divergence along the phylogeny that favours local adaptation rather than PNC.

Phylogenetic structure and molecular species delimitation hint a complex evolutionary history in an Alpine endemic Niphargus clade (Crustacea, Amphipoda)

Subterranean fauna is an important contributor to the global fauna, but it is still understudied and a large part of its taxonomy is not yet resolved. One species complex with unresolved taxonomy is the groundwater amphipod Niphargus ruffoi, endemic to the Alpine chain. Here, we used new samples from across the Alpine arc to review the taxonomic status of the entire clade, including the species N. ruffoi and Niphargus arolaensis. We sequenced four genetic markers from the collected specimens, assessed the phylogenetic position of N. ruffoi within the genus, and studied the structure of this species complex using four molecular species delimitation methods. We tested for recombination using the alignments of the concatenated nuclear rDNA genes. The phylogenetic analyses revealed high support for the monophyly of the studied species complex, defining two lineages (i.e., N. arolaensis and N. ruffoi) within the clade. Molecular species delimitation methods suggested that N. arolaensis is a single species, while N. ruffoi should be considered as a species complex of three (using ITS) to eight (using COI) putative species. Moreover, we found a discrepancy between the different nuclear ribosomal DNA markers, indicating a possible recombination with fragments of 28S DNA of N. ruffoi s. lat. present in the genome of N. arolaensis. For the above-mentioned reasons, the internal phylogenetic structure of N. ruffoi s. lat. could not be fully resolved. Moreover, no clear morphological evidence supported the molecular species delimitation. Consequently, no taxonomic changes were proposed. We postulate that this complex scenario was influenced by Pleistocene climate oscillations with subsequent fragmentation events and secondary contacts, making this an interesting study system to investigate the evolution and biogeography of Alpine clades.

Phylogeographic and Paleoclimatic Modelling Tools Improve Our Understanding of the Biogeographic History of Hierophis viridiflavus (Colubridae).

Phylogeographic and paleoclimatic modelling studies have been combined to infer the role of Pleistocene climatic oscillations as drivers of the genetic structure and distribution of Mediterranean taxa. For the European whip snake, Hierophis viridiflavus, previous studies based on paleoclimatic modelling have depicted a low reliability in the pattern of past climatic suitability across the central Mediterranean Basin, which barely fits the species' genetic structure. In this study, we combined phylogeographic and paleoclimatic modelling tools to improve our understanding of the biogeographic history of H. viridiflavus, particularly extending the sampling and phylogeographic inferences to previously under-sampled regions. Phylogeographic analyses recovered two major clades that diverged at the beginning of the Pleistocene and had diversified in different ways by the late Pleistocene: the east clade (composed of three subclades) and the west clade (with no further structure). Paleoclimatic models highlighted the temperate character of H. viridiflavus, indicating range contractions during both the last inter-glacial and last glacial maximum periods. Range expansions from southern-located climatic refugia likely occurred in the Bølling-Allerød and Middle Holocene periods, which are supported by signals of demographic growth in the west clade and South-East-North subclade. Overall, this work improves our understanding of the historical biogeography of H. viridiflavus, providing further insights into the evolutionary processes that occurred in the Mediterranean Basin hotspot.

Red deer in the Pyrenees: a risky secondary contact zone for conservation genetics

AbstractNatural events over time, and human interventions, influence the genetic structure of species. The red deer (Cervus elaphus) is widely distributed in Europe, with a large‐scale genetic structure largely determined by Pleistocene climatic oscillations. The Iberian Peninsula acted as one of the main glacial refuges for many species; a particular red deer lineage remains on the peninsula and is subjected to special conservation policies. The mountain range of the Pyrenees might be a contact zone where Iberian red deer (Cervus elaphus hispanicus) could hybridize with other central European genetic lineages. In the late twentieth century, the natural distribution areas of red deer on both sides of the Pyrenees became closer because of restocking from central Iberia to areas south of the Pyrenees and from French populations to areas north of the Pyrenees. We analyzed the genetic structure of red deer populations in the Pyrenees to investigate the underlying processes of population contact and hybridization. The analysis of microsatellite genotypes showed 2 genetic clusters. One of these clusters associated with Iberian red deer, whereas the other presented European non‐Iberian genetic composition. Migration and hybridization events occurred between both genetic clusters, mostly in the eastern part of the sampling area. The Pyrenees is currently a secondary contact zone caused by anthropogenic translocations, and a risky hybrid belt for red deer genetic conservation.

Phylogeographic structure of two sympatric species of Mediimorda Méquignon, 1946 (Mordellidae, Coleoptera)

Sympatric distribution and syntopy are not common in closely related species since sporadic crosses may lead to the formation of hybrid zones disrupting the differentiation of sympatric incipient species. In Central Spain two morphologically similar species of Mediimorda Méquignon, 1946, M. batteni Plaza-Infante, 1985 and M. bipunctata (Germar, 1827) are strictly sympatric. Mediimorda batteni is endemic to the Iberian Peninsula while M. bipunctata is widely distributed in the Western Palaearctic Region. Intriguingly, sympatric distribution among closely related taxa that exhibits little morphological variation is not common. This makes us wonder if we are really facing two independent evolutionary units of Mediimorda as previously proposed or just two phenotypic morphs of a single taxon. To test for this hypothesis, we performed Bayesian and phylogeographic analyses based on mitochondrial (cox1) and nuclear (ITS2) data and estimated divergence time of clades. Additionally, a morphological revision and construction of potential distribution models were included to determine possible niche differences. Our results corroborate the existence of two lineages well differentiated, that probably diverged during the Pliocene. According to the morphology, each clade corresponds to the previously recognized M. batteni and M. bipunctata. The absence of hybridization and ecological segregation suggests that sympatric and syntopic distribution was accomplished long time after the speciation event that separated the two taxa took place. We propose that the divergence between clades was originated by allopatric speciation during the Late Pliocene subsequently followed by range shifts during the Pleistocene climatic oscillations, which resulted in the current syntopy of the two taxa.

Geological events and climate change drive diversification and speciation of mute cicadas in eastern continental Asia

The poor mobility of nymphs living underground, usually for many years, and the weak flying ability of adults make cicadas unique for evolutionary biology and bio-geographical study. Cicadas of the genus Karenia are unusual in Cicadidae in lacking the timbals that produce sound. Population differentiation, genetic structure, dispersal and evolutionary history of the eastern Asian mute cicada Karenia caelatata were investigated based on morphological, acoustic and molecular data. The results reveal a high level of genetic differentiation in this species. Six independent clades with nearly unique sets of haplotypes corresponding to geographically isolated populations are recognized. Genetic and geographic distances are significantly correlated among lineages. The phenotypic differentiation is generally consistent with the high levels of genetic divergence across populations. Results of ecological niche modeling suggest that the potential distribution range of this mountain-habitat specialist during the Last Glacial Maximum was broader than its current range, indicating this species had benefited from the climate change during the early Pleistocene in southern China. Geological events such as orogeny in Southwest China and Pleistocene climate oscillations have driven the differentiation and divergence of this species, and basins, plains and rivers function as natural “barriers” to block the gene flow. Besides significant genetic divergence being found among clades, the populations occurring in the Wuyi Mountains and the Hengduan Mountains are significantly different in the calling song structure from other populations. This may have resulted from significant population differentiation and subsequent adaptation of related populations. We conclude that ecological differences in habitats, coupled with geographical isolation, have driven population divergence and allopatric speciation. This study provides a plausible example of incipient speciation in Cicadidae and improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this unusual cicada species. It informs future studies on population differentiation, speciation and phylogeography of other mountain-habitat insects in the East Asian continent.

Population Genetic Structure and Diversity of Cryptic Species of the Plant Genus Macrocarpaea (Gentianaceae) from the Tropical Andes.

The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial-interglacial periods are thought to have profoundly affected species distribution, richness and diversity around the world. While the effect of the PCO on population dynamics at temperate latitudes is well known, considerable questions remain about its impact on the biodiversity of neotropical mountains. Here, we use amplified fragment length polymorphism molecular markers (AFLPs) to investigate the phylogeography and genetic structure of 13 plant species belonging to the gentian genus Macrocarpaea (Gentianaceae) in the tropical Andes. These woody herbs, shrubs or small trees show complex and potentially reticulated relationships, including cryptic species. We show that populations of M. xerantifulva in the dry system of the Rio Marañón in northern Peru have lower levels of genetic diversity compared to other sampled species. We suggest that this is due to a recent demographic bottleneck resulting from the contraction of the montane wet forests into refugia because of the expansion of the dry system into the valley during the glacial cycles of the PCO. This may imply that the ecosystems of different valleys of the Andes might have responded differently to the PCO.

Population genomics reveals demographic history and selection signatures of hazelnut (Corylus).

Hazelnut (Corylus spp.) is known as one of the four famous tree nuts in the world due to its pleasant taste and nutritional benefits. However, hazelnut promotion worldwide is increasingly challenged by global climate change, limiting its production to a few regions. Focusing on the eurytopic Section Phyllochlamys, we conducted whole-genome resequencing of 125 diverse accessions from five geo-ecological zones in Eurasia to elucidate the genomic basis of adaptation and improvement. Population structure inference outlined five distinct genetic lineages corresponding to climate conditions and breeding background, and highlighted the differentiation between European and Asian lineages. Demographic dynamics and ecological niche modeling revealed that Pleistocene climatic oscillations dominantly shaped the extant genetic patterns, and multiple environmental factors have contributed to the lineage divergence. Whole-genome scans identified 279, 111, and 164 selective sweeps that underlie local adaptation in Corylus heterophylla, Corylus kweichowensis, and Corylus yunnanensis, respectively. Relevant positively selected genes were mainly involved in regulating signaling pathways, growth and development, and stress resistance. The improvement signatures of hybrid hazelnut were concentrated in 312 and 316 selected genes, when compared to C. heterophylla and Corylus avellana, respectively, including those that regulate protein polymerization, photosynthesis, and response to water deprivation. Among these loci, 22 candidate genes were highly associated with the regulation of biological quality. Our study provides insights into evolutionary processes and the molecular basis of how sibling species adapt to contrasting environments, and offers valuable resources for future climate-resilient breeding.

Climatic oscillation promoted diversification of spinous assassin bugs during Pleistocene glaciation.

Insect speciation is among the most fascinating topics in evolutionary biology; however, its underlying mechanisms remain unclear. Allopatric speciation represents one of the major types of speciation and is believed to have frequently occurred during glaciation periods, when climatic oscillation may have caused suitable habitats to be fragmented repeatedly, creating geographical isolation among populations. However, supporting evidence for allopatric speciation of insects in East Asia during the Pleistocene glaciation remains lacking. We aim to investigate the effect of climatic oscillation during the Pleistocene glaciation on the diversification pattern and evolutionary history of hemipteran insects and to test the hypothesis of Pleistocene species stability using spinous assassin bugs Sclomina (Hemiptera: Reduviidae), a small genus widely distributed in southern China but was later found to have cryptic species diversity. Here, using the whole mitochondrial genome (mitogenome) and nuclear ribosomal RNA genes, we investigated both interspecific and intraspecific diversification patterns of spinous assassin bugs. Approximate Bayesian computation, ecological niche modeling, and demographic history analyses were also applied to understand the diversification process and driven factors. Our data suggest that the five species of Sclomina are highly diverged, despite three of them currently being cryptic. Speciation occurred during the Pleistocene when suitable distribution areas were possibly fragmented. Six phylogeographic groups in the type species S. erinacea were identified, among which two groups underwent expansion during the early Last Glacial Period and after Last Glacier Maximum. Our analyses suggest that this genus may have experienced climate-driven habitat fragmentation and postglacial expansion in the Pleistocene, promoting allopatric speciation and intraspecific diversification. Our results reveal underestimated species diversity in a small insect group and illustrate a remarkable example of allopatric speciation of insects in East Asia promoted by Pleistocene climatic oscillations. These findings provide important insights into the speciation processes and aid the conservation of insect species diversity.

Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago

AbstractAimThe biodiversity of the Malay Archipelago is the product of the region's rich biogeographical history with periods of island connectivity and isolation during the Pleistocene glacial cycles. Here, the case of two endemic suid species, the Javan (Sus verrucosus) and Bawean (S. blouchi) warty pigs, was used to illustrate how biogeographic processes and recent anthropogenic pressures can shape demographic histories with significant implications for species conservation.LocationMalay Archipelago, with focus on Bawean and Java.MethodsWe employed genome‐wide single nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess interspecific genetic differentiation, to estimate divergence times and to perform demographic model selection.ResultsIn contrast to the hypothesis of recent divergence during the last glacial maximum, S. blouchi was found to have diverged from S. verrucosus at least 166 k years ago following a founder event. The contemporary S. blouchi population was characterised by a recent bottleneck that reduced the effective population size to less than 20. The genomic assessment supports the single species status of S. blouchi, as was previously proposed based on morphometrics. The demographic history of S. verrucosus showed evidence of secondary contact with the sympatric banded pig (S. scrofa vittatus) that colonised Java 70 k years ago.Main ConclusionsWhile the Javan and Bawean warty pigs have persisted throughout the Pleistocene climatic oscillations, contemporary pressures from human activities threaten their survival and immediate action should be taken to grant legal protection to both S. verrucosus and S. blouchi. This study highlighted the use of demographic history modelling using genomic data to identify evolutionary significant units and inform conservation.

Diversification and historical demography of Rhampholeon spectrum in West-Central Africa.

Pygmy Chameleons of the genus Rhampholeon represent a moderately diverse, geographically circumscribed radiation, with most species (18 out of 19 extant taxa) limited to East Africa. The one exception is Rhampholeon spectrum, a species restricted to West-Central African rainforests. We set out to characterize the geographic basis of genetic variation in this disjunctly distributed Rhampholeon species using a combination of multilocus Sanger data and genomic sequences to explore population structure and range-wide phylogeographic patterns. We also employed demographic analyses and niche modeling to distinguish between alternate explanations to contextualize the impact of past geological and climatic events on the present-day distribution of intraspecific genetic variation. Phylogenetic analyses suggest that R. spectrum is a complex of five geographically delimited populations grouped into two major clades (montane vs. lowland). We found pronounced population structure suggesting that divergence and, potentially, speciation began between the late Miocene and the Pleistocene. Sea level changes during the Pleistocene climatic oscillations resulted in allopatric divergence associated with dispersal over an ocean channel barrier and colonization of Bioko Island. Demographic inferences and range stability mapping each support diversification models with secondary contact due to population contraction in lowland and montane refugia during the interglacial period. Allopatric divergence, congruent with isolation caused by geologic uplift of the East African rift system, the "descent into the Icehouse," and aridification of sub-Saharan Africa during the Eocene-Oligocene are identified as the key events explaining the population divergence between R. spectrum and its closely related sister clade from the Eastern Arc Mountains. Our results unveil cryptic genetic diversity in R. spectrum, suggesting the possibility of a species complex distributed across the Lower Guinean Forest and the Island of Bioko. We highlight the major element of species diversification that modelled today's diversity and distributions in most West-Central African vertebrates.