Phylogeographic Break Research Articles

Across a phylogeographic break in the Qinling Mountains-Huaihe River Line: Quaternary evolutionary history of a medicinal and edible homologous plant (Allium macrostemon) in China

Biogeographic barriers to gene flow are central to studies of plant phylogeography. There are many physical and geographic barriers in China, but few studies have used molecular ecological evidence to investigate the natural geographic isolation barrier of the Qinling Mountains-Huaihe River Line (QHL). Allium macrostemon is a precious Chinese perennial herb belonging to the Amaryllidaceae family. It is used as a food and medicine, with a variety of health and healing properties. Five SSR markers, three chloroplast DNA (cpDNA) markers (psbA-trnH, rps16 and trnL-F), one nuclear ribosomal DNA (nrDNA) marker (ITS), and simplified genome GBS sequencing were used to analyse the genetic diversity and structure of A. macrostemon. Combining SSR, cpDNA, nrDNA ITS data and GBS analysis results, we divided A. macrostemon populations into northern and southern groups, with the southern group further divided into southwestern and central-southeastern groups. Niche simulation results reveal that the distribution area of A. macrostemon will reach its maximum in the future. These data indicate that the regional separation of A. macrostemon has been maintained by the combined influence of a geographical barrier and Quaternary climate, and that the back-and-forth fluctuations of QHL and Quaternary climate have played an important role in this process. QHL acts as a north-south dividing line in phylogeography and population genetic structure, promoting physical geographic isolation. This study provides a theoretical basis for the conservation, development, and utilization of A. macrostemon resources. It further provides a reference for understanding the systematic geographical pattern of the large-scale spatial distribution of plants in China and enriches our understanding of Quaternary plant evolution in areas with complex terrain.

The Great Rift Valley is a more pronounced biogeographic barrier than the Blue Nile Valley for six Ethiopian Highland passerines in the eastern Afromontane biodiversity hotspot

ABSTRACT The Ethiopian Highlands are divided by lowland biogeographic barriers, including the Blue Nile Valley (BNV) and Great Rift Valley (GRV). We show that the GRV is a more pronounced phylogeographic break than the BNV for 6 focal passerines. Previous research suggests that the BNV greatly shaped phylogeographic patterns in relatively sedentary montane taxa such as frogs and rodents, whereas the GRV shaped phylogeographic patterns in volant taxa such as birds. However, no previous research simultaneously compares the impact of each valley on phylogeographic patterns in birds, and as these barriers vary in geographic extent and topography, the relative extent of their effects on gene flow is unclear. Using whole-genome resequencing, we quantified genetic variation in 6 montane forest passerines in the Ethiopian Highlands and found that their phylogeographic patterns varied, with general trends distinct from those of taxa that were previously studied across the same barriers. Genetic variation was assessed by estimating genome-wide genetic diversity (HO), demographic history, phylogeographic structure, and phylogeographic concordance among taxa. Population pairs flanking the GRV showed higher FST and more distinct population clusters in principal component analysis than those separated by the BNV. HO was broadly consistent across populations, excluding noticeable reductions in 2 populations (1 population each in 2 separate species). The overall phylogenetic signature and concordance across study taxa supported populations separated by the BNV as sister and populations southeast of the GRV as most distinct.

Historical imprints on genetic population structure in direct-developing beach whelks (Bullia digitalis)

Marine organisms often show deep genetic divergence between lineages that are characterized by shallow population structure. The distinction of historical and contemporary demographic forces in creating and maintaining these genetic patterns is crucial for management and conservation. In this study, we examined the genetic population structure of Bullia digitalis, a lecithotrophic sandy beach whelk that lacks a pelagic larval phase and is thus expected to show limited connectivity between populations. Mitochondrial (mt)DNA cytochrome c oxidase subunit I (COI; 540 bp, n = 214) and a reanalysis of allozyme data (14 loci, n = 735) among populations along the cool southeast Atlantic (west) and warm-temperate southwest Indian Ocean (south) coasts of southern Africa showed a strong phylogeographic break across Cape Point with mtDNA (ΦRT = 0.6, p < 0.001), but a weak break with allozymes (FRT = 0.002, p = 0.004). MtDNA gene flow occurred asymmetrically from the west to the south coast. Although there was no mtDNA differentiation between populations on either side of that break (ΦSR = 0.0), there was weak but significant isolation by distance (IBD) among south coast samples (r2 = 0.20, p = 0.039). In contrast, significant allozyme differentiation was detected on small spatial scales but without overall IBD. MtDNA mismatch analysis indicated a recent range expansion, suggesting historic population expansions, most likely during periods of lower sea levels and greater habitat continuity along southern African shores. Thus, the apparent mtDNA connectivity among populations of beach whelks likely reflects historic, rather than contemporary, gene flow.

Cryptic diversity in southern African kelp

The southern coast of Africa is one of the few places in the world where water temperatures are predicted to cool in the future. This endemism-rich coastline is home to two sister species of kelps of the genus Ecklonia maxima and Ecklonia radiata, each associated with specific thermal niches, and occuring primarily on opposite sides of the southern tip of Africa. Historical distribution records indicate that E. maxima has recently shifted its distribution ~ 70 km eastward, to sites where only E. radiata was previously reported. The contact of sister species with contrasting thermal affinities and the occurrence of mixed morphologies raised the hypothesis that hybridization might be occurring in this contact zone. Here we describe the genetic structure of the genus Ecklonia along the southern coast of Africa and investigate potential hybridization and cryptic diversity using a combination of nuclear microsatellites and mitochondrial markers. We found that both species have geographically discrete genetic clusters, consistent with expected phylogeographic breaks along this coastline. In addition, depth-isolated populations were found to harbor unique genetic diversity, including a third Ecklonia lineage. Mito-nuclear discordance and high genetic divergence in the contact zones suggest multiple hybridization events between Ecklonia species. Discordance between morphological and molecular identification suggests the potential influence of abiotic factors leading to convergent phenotypes in the contact zones. Our results highlight an example of cryptic diversity and hybridization driven by contact between two closely related keystone species with contrasting thermal affinities.

Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen (Populus rotundifolia) in the Hengduan Mountains

Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia, a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China. Demographic and migration hypotheses were tested using coalescent-based approaches. Limited historical gene flow was observed between the western and eastern groups of P. rotundifolia, but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line, manifesting in clear admixture and high genetic diversity in the central group. Wind-borne pollen and seeds may have facilitated the dispersal of P. rotundifolia following prevalent northwest winds in the spring. We also found that the Hengduan Mountains, where multiple genetic barriers were detected, acted on the whole as a barrier between the western and eastern groups of P. rotundifolia. Ecological niche modeling suggested that P. rotundifolia has undergone range expansion since the last glacial maximum, and demographic reconstruction indicated an earlier population expansion around 600 Ka. The phylogeographic pattern of P. rotundifolia reflects the interplay of biological traits, wind patterns, barriers, niche differentiation, and Quaternary climate history. This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.

Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli

The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.

Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China.

Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.

Opposing genetic patterns of range shifting temperate and tropical gastropods in an area undergoing tropicalisation

AbstractAimThe poleward range expansion of tropical species, and range contraction of temperate species (known as tropicalisation) has mainly been studied from an ecological perspective, with little research on its genetic consequences. Here, we used distributional and genetic data to document the consequences of tropicalisation in rocky shore gastropods and assess more broadly the future implications of tropicalisation on phylogeographic patterns.LocationNineteen sampling sites along >3000 km of the eastern Pacific rocky intertidal zone, from the tip of the Baja California Peninsula to southern California.TaxonTemperate gastropods: Lottia conus, L. strigatella, Fissurella volcano and Tegula gallina.Tropical gastropods: Fissurella rubropicta, Nerita funiculata and N. scabricosta.MethodsWe determine historical and modern distributions of tropical and temperate species by combining historical records with current field surveys. Using a section of the cytochrome oxidase subunit I gene, we utilised comparative phylogeography, analysis of molecular variance, FST pairwise comparison, mismatch distributions of haplotype differences and neutrality tests to detect genetic signatures of tropicalisation and to better understand its consequences.ResultsWe identified range contractions in two temperate species and range expansion in all three tropical species. We detected genetic signatures of range expansion in the tropical species through unimodal distributions of pairwise haplotype differences and strongly negative values for the Fu and Li D and F* statistics. We found population subdivision and phylogeographic breaks in three temperate species, although the geographic location of the breaks differed among species.Main ConclusionsGenetic signatures and field surveys indicate recent range expansions in tropical species, supporting tropicalisation along the studied coastline. Conversely, we found phylogeographic breaks in temperate species, suggesting that tropicalisation may cause genetic erosion of evolutionary distinct lineages with range‐contraction. The different locations of the phylogeographic breaks among temperate species suggests that some barriers are species specific.

Congruence between microsatellite loci, SNPs, and COI gene reveals a phylogeographic break in the southern Caribbean Sea: The case of West Indian top shell Cittarium pica (Gastropoda: Tegulidae)

It has been proposed that species associated with shallow rocky bottoms in the southern Colombian Caribbean Sea are affected by two biogeographic barriers: the Magdalena River plume (MRP) and the combination of the absence of rocky bottoms and the almost permanent upwelling in the Guajira peninsula (ARB+PUG). We evaluated whether these barriers had generalized genomic effects on the phylogeographic structure of the West Indian top shell (Cittarium pica), a crucial fishery resource in many areas of the Caribbean Sea. Ten species-specific microsatellite loci, 55,112 SNPs from ddRADseq, and COI gene were used on samples of C. pica collected at five Colombian localities (Cabo de la Vela; Santa Marta; Cartagena; Isla Fuerte; and Capurganá). Genetic structure analyses performed for microsatellite and SNP loci indicated that there are three genetic groups of C. pica in Colombia (pop 1: Cabo de la Vela; pop 2: Santa Marta; pop 3: Cartagena+Isla Fuerte+Capurganá). However, both SNPs and COI gene were congruent in showing a phylogeographic break caused by only the ARB + PUG (AMOVA: ΦCT-SNP=0.224, p < 0.05; ΦCT-COI=0.722, p < 0.05), which was confirmed by the maximum-likelihood and network trees. In contrast, MRP was shown to be a permeable barrier to gene flow. Demographic history analysis indicated that C. pica experienced historical changes in population size during the last glaciation period. Cittarium pica is a biological model to demonstrate how the ARB + PUG barrier could affect marine organisms living in shallow rocky habitats, mainly those lacking larvae or having a short-lived larval phase in the southern Caribbean Sea. Finally, some recommendations for fisheries management and conservation C. pica populations are discussed.

Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal

Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal

Effects of Quaternary climatic oscillations over the Chacoan fauna: phylogeographic patterns in the southern three-banded armadillo Tolypeutes matacus (Cingulata: Chlamyphoridae)

Abstract The southern three-banded armadillo, Tolypeutes matacus, is one of the most representative species of the South American Chaco region. The susceptibility of this species to climatic changes and its good number of paleontological records has led to the study of their range dynamics for untangling the effects of Quaternary oscillations. These studies yielded contradictory results, suggesting expansion processes under opposite conditions: some during glacial periods and others during interglacial periods. Here, we assess the population structure of T. matacus in Argentina based on mitochondrial genes, and estimate demographic and spatial dynamics that contribute to unveiling the evolutionary process that moulded its biogeography. We found no clear phylogeographical breaks, although there were differences in the composition and frequency of haplotypes between the northern and southern localities studied. Demographic inferences indicate that the species has undergone population and range expansion processes. The higher diversity found in the north and the spatial diffusion analysis allow us to infer a north–south direction of this expansive process. Our results yield essential evidence for disentangling the evolution of this Chacoan species linked with Quaternary climates and provide genetic information about its populations that should be taken into account for the conservation of this threatened mammal.

A Comparative Phylogeography of Three Marine Species with Different PLD Modes Reveals Two Genetic Breaks across the Southern Caribbean Sea.

The comparative phylogeography of marine species with contrasting dispersal potential across the southern Caribbean Sea was evaluated by the presence of two putative barriers: the Magdalena River plume (MRP) and the combination of the absence of a rocky bottom and the almost permanent upwelling in the La Guajira Peninsula (ARB + PUG). Three species with varying biological and ecological characteristics (i.e., dispersal potentials) that inhabit shallow rocky bottoms were selected: Cittarium pica (PLD < 6 days), Acanthemblemaria rivasi (PLD < 22 days), and Nerita tessellata (PLD > 60 days). We generated a set of SNPs for the three species using the ddRad-seq technique. Samples of each species were collected in five locations from Capurganá to La Guajira. For the first time, evidence of a phylogeographic break caused by the MRP is provided, mainly for A. rivasi (AMOVA: ΦCT = 0.420). The ARB + PUG barrier causes another break for A. rivasi (ΦCT = 0.406) and C. pica (ΦCT = 0.224). Three populations (K = 3) were identified for A. rivasi and C. pica, while N. tessellata presented one population (K = 1). The Mantel correlogram indicated that A. rivasi and C. pica fit the hierarchical population model, and only the A. rivasi and C. pica comparisons showed phylogeographic congruence. Our results demonstrate how the biological traits of these three species and the biogeographic barriers have influenced their phylogeographic structure.

A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea-Baltic Sea transition zone.

Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about this community. Here, we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both microbiomes, but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea driven by changes in the frequency of different groups of known polysaccharide degraders. We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the different seaweed communities. Our results reveal the complexities of both the wrackbed microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.

Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species.

Mountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple million years are usually assumed to play an important role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ecological Niche Modelling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of codistributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, c. 21 thousand years ago), although we could not obtain a clear demographic pattern for the animal lineages. We also obtained a signal of a congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço's biota.

Neogene–Quaternary tectonic, eustatic and climatic events shaped the evolution of a South American treefrog

AbstractAimUnderstanding how past geological and climatic events could have generated intraspecific genetic variation at different temporal and spatial scales in the Neotropics requires a model encompassing distinct ecoregions. Because Anura species have their evolutionary history affected by climate and environmental changing, it is a suitable model to investigate the signatures of Neotropical historical events in species populations. Here we used a treefrog species to test hypotheses associated with tectonic, eustatic and climatic events along with isolation‐by‐environment and isolation‐by‐distance spatial patterns in genetic diversity.TaxonScinax squalirostris (Lutz, 1925), Anura: Hylidae.LocationAtlantic Forest, Cerrado, Chaco, Uruguayan Savanna and Pampas ecoregions in South America.MethodsWe sequenced nuclear and mitochondrial data from 219 individuals of S. squalirostris sampled at 26 locations in South America. We performed statistical phylogeographic analyses and reconstruction of spatiotemporal dispersal dynamics. Ecological niche modelling was conducted to predict spatial changes in environmental suitability from the Last Glacial Maximum to the Holocene and present day.ResultsWe recovered a significant phylogeographic break roughly dated back to the Miocene (~7.6 Ma), coinciding with the retraction of marine incursions in the Paraná basin. Most dispersal events occurred in cooler periods of the Pliocene–Pleistocene transition. The spatial pattern in genetic diversity was not correlated with geographical distance or environmental variables.Main ConclusionsScinax squalirostris had a quasi‐stable distribution through time. Neogene–Quaternary tectonic, eustatic and climatic events drove the demographic history and dispersal dynamics of species, with a phylogeographical break dated to the Miocene coinciding with retractions of marine incursions in the Paraná basin. Lineage dispersal spread from the southern Atlantic Forest and retrieved gene flow signals congruent with the cold periods of the Pliocene and Pleistocene.

Climate Cycles, Habitat Stability, and Lineage Diversification in an African Biodiversity Hotspot

The Eastern Arc Mountains of Tanzania and Kenya, a montane archipelago of 13 uplifted fault blocks (sky islands) isolated by lowland arid savanna, are a center of exceptional biological endemism. Under the influence of humid winds from the Indian Ocean, forests and associated species may have persisted in this region since the final uplift of these blocks in the late Miocene. Today, these mountains are inhabited by a remarkable diversity of bird species. To better understand the evolutionary processes behind this diversity, we combined molecular phylogenetic studies of East African montane birds with paleoclimate modeling of its montane forests. Across its largest lowland barrier, the 125 km between the Usambara and Nguru/Nguu Mountains, 10 of the 14 bird lineages exhibited a phylogeographic break. Using Bayesian methods, we established that at least three periods of forest contraction and expansion affected the diversification of Eastern Arc birds. Habitat distribution models suggest that lower-elevation hills may have acted as stepping-stones connecting isolated highlands to allow for the dispersal of montane forest-dependent species across them. Periods of vicariance during paleoclimatic cycles extending back through the Last Glacial Maximum would have then isolated these populations within the highlands they had reached. The broad distribution of neoendemic species across the mountains of East Africa provides evidence of climate cycling as a driver of lineage diversification. The high incidence of narrow-range endemism of paleoendemic species on the Usambara, Uluguru, and Udzungwa Mountains of this region is harder to explain. Our paleoclimate models retrodicted the persistence of montane forest during climate cycles on several Eastern Arc sky islands but not on the Southern Tanzania Volcanic Highlands. Consistent with recent theoretical work, different rates of local extinction rather than increased rates of lineage diversification may explain the pattern of excessive narrow-range endemism on some sky islands over others. Thus, a regional filtering effect is generated, with paleoendemics maintaining populations through time only in areas where habitat persisted, providing a credible explanation for the dramatic variance in levels of endemism among different East African sky islands.

Contrasting patterns of population structure of Bulwer’s petrel (Bulweria bulwerii) between oceans revealed by statistical phylogeography

The patterns of population divergence of mid-latitude marine birds are impacted by only a few biogeographic barriers to dispersal and the effect of intrinsic factors, such as fidelity to natal colonies or wintering grounds, may become more conspicuous. Here we describe, for the first time, the phylogeographic patterns and historical demography of Bulwer’s petrel Bulweria bulwerii and provide new insights regarding the drivers of species diversification in the marine environment. We sampled Bulwer’s petrels from the main breeding colonies and used a statistical phylogeography approach based on surveying nuclear and mitochondrial loci (~ 9100 bp) to study its mechanisms of global diversification. We uncovered three highly differentiated groups including the Western Pacific, the Central Pacific and the Atlantic. The older divergence occurred within the Pacific Ocean, ca. 850,000 ya, and since then the W Pacific group has been evolving in isolation. Conversely, divergence between the Central Pacific and Atlantic populations occurred within the last 200,000 years. While the Isthmus of Panama is important in restricting gene flow between oceans in Bulwer’s petrels, the deepest phylogeographic break is within the Pacific Ocean, where oceanographic barriers are key in driving and maintaining the remarkable structure found in this highly mobile seabird. This is in contrast with the Atlantic, where no structure was detected. Further data will provide insights regarding the extent of lineage divergence of Bulwer’s petrels in the Western Pacific.

Ancient vicariance is reinforced by adaptive divergence in the southern beech: Contributions from geogenomics

AbstractAimGeogenomics seeks to understand geological processes linked to lineage divergence. However, the mechanisms that conserve ancient signals in spite of gene flow are still unclear. In the southern beech, the deep lineage divergence produced by vicariant events is associated with ancient marine transgressions. We hereby evaluate the hypothesis that this divergence is maintained by diversifying selection.LocationSouthern Argentina and Chile.Taxon Nothofagus dombeyi. MethodsThe lineage divergence by means of analysis of molecular variance (AMOVA), principal coordinate analysis, assignment tests and multiple matrix regression analyses were assessed using chloroplast DNA and neutral and outlier single nucleotide polymorphisms (SNPs). Several environmental variables were used to characterize potential within‐species niche structuring and genotype–environment associations.ResultsTwo deep‐rooted latitudinally structured lineages resulted from cpDNA, the northern cluster being more genetically diverse than the southern one. Of the total of 2943 SNPs, 33 identified as outliers and produced two genetic clusters. Neutral SNPs yielded no structure by AMOVA, whereas higher (&gt;75%) FST values were obtained for cpDNA and outlier SNPs. Precipitation variables were mostly associated with population clusters and suggested two climatic niches, consisting of cold and dry in the south and more variable precipitation, temperature and soil conditions in the north. Associations of genetic distance with environment and geography suggested isolation‐by‐distance and isolation‐by‐ecology or isolation‐by‐environment effects.Main conclusionsAncient lineage divergence in N. dombeyi, originally driven by vicariance, has been maintained by diversifying selection under distinct environmental conditions that also define distinct within‐species niches. Deeply rooted phylogeographical breaks can be conserved in continuously distributed species in the absence of current geographical barriers. Yet, physical gradients exert differential selective pressures, which are maintained in the face of potential gene flow. As a result, selection can lead to geographically localized and differentially adapted groups of populations that can be detected by a combination of traditional phylogeographical and novel genomic methods.

Diversification of Amazonian spiny tree rats in genus Makalata (Rodentia, Echimyidae): Cryptic diversity, geographic structure and drivers of speciation.

Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes.

Wind-dispersed seeds blur phylogeographic breaks: The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin

The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits. Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants. Here, we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa, a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China. We sequenced and analyzed three plastid DNA fragments (ptDNA) and eight nuclear microsatellites (nSSRs) of 265 individuals of P. lasiocarpa from 21 populations spanning the entire distribution range. Distribution patterns based on nSSR data revealed that there are three genetic groups in P. lasiocarpa. This is consistent with the three phylogeographic breaks (Sichuan Basin, the Kaiyong Line and the 105°E line), where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups. However, the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks, and wind-dispersed seeds may be one of the main contributing factors. Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial. A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages. These results indicate that biological traits are likely to affect the evolutionary history of plants, and that nuclear molecular markers, which experience higher levels of gene flow, might be better indicators of phylogeographic breaks.