Spatial Genetic Analyses Research Articles

Sex-biased dispersal patterns of a social passerine: complementary approaches and evidence for a role of spatial scale

AbstractAnimal dispersal patterns have important implications for many biological processes, but the measurement of dispersal is challenging and often requires the use of complementary approaches. In this study, we investigated the local-scale sex-biased dispersal pattern in a social bird, the black-throated tit (Aegithalos concinnus), in central China. Spatial genetic autocorrelation analyses suggested that significant fine-scale genetic structure existed in males but not in females. Mark–recapture analyses of ringed individuals also showed that female offspring were more dispersive than male offspring, supporting genetic evidence of local female-biased dispersal. These results were contrary to a previous finding of male-biased long-distance dispersal in this species that was based on analyses of gene flow across the species range in China. This implies that the species might potentially have a scale-dependent dispersal strategy, with females frequently dispersing further than males at the local level, but with a proportion of males occasionally dispersing over long distances and contributing more to gene flow at a larger geographical scale. Long-distance dispersal by male black-throated tits might be induced by competition for resources or by unfavourable environmental conditions, warranting further investigation, but our findings increase the evidence that geographical scale is an important factor to be considered when investigating animal dispersal patterns.

To what extent are bryophytes efficient dispersers?

Abstract Bryophytes are typically seen as extremely efficient dispersers. Experimental evidence suggests that efficient short‐distance dispersal coupled with random long‐distance dispersal (LDD) leads to an inverse isolation effect. Under the latter, a higher genetic diversity of colonizing propagules is expected with increasing isolation, counteracting differentiation beyond the range of short‐distance dispersal. This expectation is tested from a review of evidence on spatial genetic structure and analyses of isolation‐by‐distance (IBD) at different scales. A decay of the IBD signal, characterized by non‐significant slopes between kinship coefficients and geographic distance was observed beyond 100 m. A second slope shift was observed at distances larger than 1 km, with a proportion of significant slopes in more than one third of the datasets. The decay of the IBD signal beyond 100 m, which reflects efficient LDD, is consistent with the inverse isolation hypothesis. Persistence of a significant IBD signal at medium ranges in one third of the analysed cases suggests, however, that the inverse isolation effect is not a rule in bryophyte spore dispersal. Furthermore, the higher proportion of significant IBD patterns observed at scales over 100 km likely marks the limits of regional dispersal, beyond which an increasingly smaller proportion of spores travel. Synthesis. We discuss the differences between experimental and genetic estimates of spore dispersal and conclude that geographic distance remains a significant proxy of spore colonization rates, with major consequences for our understanding of actual migration capacities in bryophytes, and hence, our capacity to model range shifts in a changing world.

Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster.

Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across the species' range using a small panel of single nucleotide polymorphisms (SNPs) previously isolated from restriction‐site‐associated DNA sequencing; these SNPs were selected to maximize differentiation at a range of both broad and fine scales. After quality control and filtering, 1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The results revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea. In addition, a genetic cline across the north‐east Atlantic was revealed using both putatively neutral and outlier SNPs, but the precise driver(s) of this clinal pattern—isolation by distance, secondary contact, selection across an environmental gradient, or a combination of these factors—remains undetermined. Putatively neutral markers differentiated lobsters from Oosterschelde, an estuary on the Dutch coast, a finding likely explained by past bottlenecks and limited gene flow with adjacent North Sea populations. Building on the findings of our spatial genetic analysis, we were able to test the accuracy of assigning lobsters at various spatial scales, including to basin of origin (Atlantic or Mediterranean), region of origin and sampling location. The predictive model assembled using 79 SNPs correctly assigned 99.7% of lobsters not used to build the model to their basin of origin, but accuracy decreased to region of origin and again to sampling location. These results are of direct relevance to managers of lobster fisheries and hatcheries, and provide the basis for a genetic tool for tracing the origin of European lobsters in the food supply chain.

Mitochondrial phylogeography of kinkajous (Procyonidae, Carnivora): maybe not a single ESU

AbstractKnowledge of how a species is divided into different genetic units, and the structure among these units, is fundamental to the protection of biodiversity. Procyonidae was one of the families in the Order Carnivora with more success in the colonization of South America. The most divergent species in this family is the kinkajou (Potos flavus). However, knowledge of the genetics and evolution of this species is scarce. We analyzed five mitochondrial genes within 129 individuals of P. flavus from seven Neotropical countries (Mexico, Guatemala, Honduras, Colombia, Ecuador, Peru, and Bolivia). We detected eight different populations or haplogroups, although only three had highly significant bootstrap values (southern Mexico and Central America; northern Peruvian, Ecuadorian, and Colombian Amazon; and north-central Andes and the southern Amazon in Peru). Some analyses showed that the ancestor of the southern Mexico–Central America haplogroup was the first to appear. The youngest haplogroups were those at the most southern area analyzed in Peru and Bolivia. A “borrowed molecular clock” estimated the initial diversification to have occurred around 9.6 million years ago (MYA). All the spatial genetic analyses detected a very strong spatial structure with significant genetic patches (average diameter around 400–500 km) and a clinal isolation by distance among them. The overall sample and all of the haplogroups we detected had elevated levels of genetic diversity, which strongly indicates their long existence. A Bayesian Skyline Plot detected, for the overall sample and for the three most significant haplogroups, a decrease in the number of females within the last 30,000–50,000 years, with a strong decrease in the last 10,000–20,000 years. Our data supported an alignment of some but not all haplogroups with putative morphological subspecies. We have not discounted the possibility of a cryptic kinkajou species.

Ups and downs: Genetic differentiation among populations of the Podocarpus (Podocarpaceae) species in Mesoamerica

The biogeographical history of Mesoamerican cloud forests is complex, encompassing a diverse and heterogeneous mixture of species with temperate and tropical origins. The dynamic geological landscape and climate change from the Miocene to the Pleistocene affected the distributions and composition of cloud forests in the region, and contributed to divergence events at different time scales. We assessed genetic variation of 29 populations of P. matudae, and closely related P. guatemalensis and P. oleifolius (Podocarpaceae) by sequencing 255 samples of the psbA-trnH and trnL-F intergenic spacer regions across the species ranges. We conducted phylogenetic, population and spatial genetic analyses as well as divergence time estimation and ecological niche modelling (ENM) to test the generality of demographic and genetic scenarios for cloud forest-adapted species. The results revealed genetic differentiation among species, with some individuals of P. oleifolius and P. guatemalensis placed in the P. matudae group and some P. oleifolius in the P. guatemalensis group. Predictions of ENMs under past climatic conditions and a strong signal of spatial expansion suggest that the highland P. matudae and P. oleifolius populations experienced expansions into lower elevation during the Last Glacial Maximum (LGM). Contrary to predictions by the two precipitation models and elevational ups and downs for cloud forest taxa during the LGM, genetic differentiation and predicted distribution of suitable habitat support the hypotheses that P. matudae and P. oleifolius remained in situ during the LGM primarily within the current fragmented distribution of the cloud forest and spread into the lowlands during the LGM, whereas the distribution of suitable habitat for P. guatemalensis had no major changes upwards from the Last Inter Glacial (LIG) to current conditions.

The First Molecular and Phenotypic Characterization of the Invasive Population of Aedes albopictus (Diptera: Culicidae) from the Central Balkans.

Aedes (Stegomya) albopictus (Skuse 1984), the Asian tiger mosquito, represents the most invasive and one of the medically most important mosquito vectors. Although native to South East Asia, the species has recently spread globally, and was registered in the city of Novi Sad (Serbia, Central Balkans) in August 2018. We characterized the invasive population using phenotypic (wing size and shape) and molecular (nuclear, internal transcribed spacer 2- ITS2, and mitochondrial, cytochrome c oxidase subunit I- COI) markers. The results of phenotypic analyses indicated that the Serbian population could be differentiated from the native (Thailand) and invasive (Hawaii and Florida) populations due to restricted gene flow, founder effect, and supposed different strain origin. The Serbian population showed genetic homogeneity, indicative of a small founder number (bottleneck invasion model). Despite the incorporation of ITS2 GenBank sequences into the data set, neither spatial (Geneland) nor nonspatial (BAPS) genetic structuring analyses helped infer the Serbian population origin. However, the comparison of the retrieved COI haplotype with previously characterized mitogenomes indicated a temperate strain origin, capable of overwintering. Such findings suggest that the newly registered Ae. albopictus population could be able to establish itself since previous studies outlined Novi Sad as a suitable area.

Chromosome polymorphisms track trans-Atlantic divergence and secondary contact in Atlantic salmon.

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) in the western and eastern Atlantic diverged >600,000years before present, with the two lineages isolated in different southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic divergence. Here, we investigate the genomic consequences of glacial isolation and trans-Atlantic secondary contact using 108,870 single nucleotide polymorphisms genotyped in 80 North American and European populations. Throughout North America, we identified extensive interindividual variation and discrete linkage blocks within and between chromosomes with known trans-Atlantic differences in rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post-glacial trans-Atlantic secondary contact, contrasting with low European ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intrapopulation diversity, suggesting a derived chromosome fusion polymorphism that evolved within North America. Evidence of potential selection on both genomic regions suggests that the adaptive role of rearrangements warrants further investigation in Atlantic salmon. Our study highlights how Pleistocene glaciations can influence large-scale intraspecific variation in genomic architecture of northern species.

Spatial genetic analysis of coyotes in New York State

ABSTRACTThe robust dispersal capability of the coyote (Canis latrans) would suggest a pattern of widespread gene flow across North America, yet historical legacies, dispersal barriers, and habitat affinities may produce or reinforce genetic structure. In the northeastern United States, some coyotes carry genetic signatures from past hybridization events with eastern wolves (C. lupus lycaon). These so‐called “coywolves” may have differential predation or competitive success compared with the western origin coyotes with whom they share the contemporary landscape. We sampled coyote populations from New York (n = 156) and Wyoming, USA (n = 8) in 2006–2007 and from South Carolina, USA, in 2010 and confirmed regional genetic structure among these coyote populations. Then, within the putative contact zone between the northeastern and western coyote colonization fronts (New York State), we evaluated evidence for broad‐ and fine‐sale genetic structure, and a genetic gradient among New York coyotes using a suite of spatial genetic analyses. Although broad‐scale analyses indicated New York coyotes were highly intermixed, subtle isolation‐by‐distance was detected, and local spatial autocorrelation indicated potentially shorter dispersal distances and larger group sizes for coyotes in the Northeastern Highlands (Adirondack Mountains and foothills). Yet we failed to detect a distinct contact zone between 2 coyote types in New York, indicating that local abundance and ecological context rather than genetic lineage are likely to determine the local ecological effects of coyotes in this region. We suggest that the contact zone between coyote colonization fronts has either eroded or moved further south. © 2019 The Wildlife Society.

Population genetic structure and geographical variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae).

BackgroundNeotricula aperta is the snail-intermediate host of the parasitic blood-fluke Schistosoma mekongi which causes Mekong schistosomiasis in Cambodia and the Lao PDR. Despite numerous phylogenetic studies only one DNA-sequence based population-genetic study of N. aperta had been published, and the origin, structure and persistence of N. aperta were poorly understood. Consequently, a phylogenetic and population genetic study was performed, with addition of new data to pre-existing DNA-sequences for N. aperta from remote and inaccessible habitats, including one new taxon from Laos and 505 bp of additional DNA-sequence for all sampled taxa,.Principal findingsSpatial Principal Component Analysis revealed the presence of significant spatial-genetic clustering. Genetic-distance-based clustering indicated four populations with near perfect match to a priori defined ecogeographical regions. Spring-dwelling taxa were found to form an ecological isolate relative to other N. aperta. The poor dispersal capabilities suggested by spatial-genetic analyses were confirmed by Bayesian inference of migration rates. Population divergence time estimation implied a mid-Miocene colonisation of the present range, with immediate and rapid radiation in each ecogeographical region. Estimated effective population sizes were large (120–310 thousand).ConclusionsThe strong spatial-genetic structure confirmed the poor dispersal capabilities of N. aperta—suggesting human-mediated reintroduction of disease to controlled areas as the primary reason for control failure. The isolation of the spring-dwelling taxa and ecogeographical structure suggests adaptation of sub-populations to different habitats; the epidemiological significance of this needs investigation. The large effective population sizes indicate that the high population densities observed in surveyed habitats are also present in inaccessible areas; affording great potential for recrudescence driven by animal-reservoir transmission in remote streams. Mid-Miocene colonisation implies heterochronous evolution of these snails and associated schistosomes and suggests against coevolution of snail and parasite. Heterochronicity favours ecological factors as shapers of host-parasite specificity and greater potential for escape from schistosomiasis control through host-switching.

Carapace shape variation of genetically divergent populations of Testudo hermanni boettgeri (Reptilia: Testudines)

The published cytb mtDNA sequences from a previous phylogeographic study of Testudo hermanni and de novo genetic and phenotypic data of samples from the Pcinja River Valley (Serbia, Central Balkans) and Trebinje (Bosnia and Herzegovina) were used to: (i) genetically characterize samples from Pcinja, a region of great importance from the conservation standpoint due to its taxonomic diversity and biogeographical history, and Trebinje, a type locality of a disputed taxon ?Testudo hercegoviensis? Werner, 1899; (ii) to study the link between gene genealogy and geographic distribution by implementing spatial genetic analyses, and (iii) to assess whether the distribution of carapace shape variation is in accordance with genetic clusters. The samples from Pcinja and Trebinje possessed divergent haplotypes that corresponded to east (HI) and west (HV) genetic clusters, respectively. Geometric morphometrics was found to be a suitable method to distinguish divergent genetic clusters, arguing for the reassessment of a subspecific ranking within the currently recognized eastern Hermann?s subspecies, T. h. boettgeri.

Spatial genetic analysis of roe deer from the northern Serbian Province of Vojvodina

Spatial genetic analysis of roe deer from the northern Serbian Province of Vojvodina

Mitogenomics of the jaguarundi (Puma yagouaroundi, Felidae, Carnivora): Disagreement between morphological subspecies and molecular data

We analyzed 80 mitogenomes of the elusive jaguarundi (Puma yagouaroundi, Felidae, Carnivora), representing seven of the eight putative morphological subspecies traditionally described. The mitochondrial genetic diversity levels were very high in this cat species and therefore similar to other Neotropical cats. Nonetheless, the number of significantly different molecular clusters did not align well with putative morphological subspecies. We detected three possible molecular subspecies: P. y. yagouaroundi (wide distribution in Central and South America), P. y. melantho (Central Andean, and their inter-valleys, Peruvian area) and P. y. eyra (Paraguay and northern Argentina). There were also small geographical clusters with no correspondence with the morphological subspecies, especially in Costa Rica, northern and eastern Colombia, and Pacific trans-Andean Colombia and Ecuador. Thus, the number of molecular subspecies in jaguarundi could be less than the number defined morphologically. However, well-differentiated mitochondrial lineages could exist in the area of the putative P. y. panamensis and correspond to undescribed subspecies. The temporal split of the ancestors of the puma and jaguarundi and the initial mitochondrial diversification within the jaguarundi occurred during the late Pliocene, but the major fraction of haplotype proliferation happened during the Pleistocene. All the procedures we used detected a strong population expansion for the jaguarundi during the Günz-Mindel interglacial period of the Pleistocene. The spatial genetic analyses showed that the isolation-by-distance patterns are not well developed in this species. In contrast, we detected a very significant circular cline with spatial autocorrelation. Therefore, from a molecular perspective some of the individuals far removed from each other geographically are also very similar. This new information may be very helpful to conservation ecologists and managers of jaguarundi habitats as we continue to improve our understanding of the evolutionary history of this cat species.

Population structure of Guyanagaster necrorhizus supports termite dispersal for this enigmatic fungus.

Understanding how species accomplish dispersal of their propagules can shed light on how they are adapted for their ecosystem. Guyanagaster necrorhizus is a sequestrate fungus, meaning its dispersal propagules, or spores, are entirely enclosed within a fruiting body, termed a sporocarp. This fungus is most closely related to Armillaria and its allies. While Armillaria species form mushrooms and have forcibly discharged spores, G.necrorhizus spores have lost this ability, and by necessity, must be passively dispersed. However, G.necrorhizus does not possess characteristics of other sequestrate fungi with known dispersal mechanisms. Repeated observations of termites feeding on G.necrorhizus sporocarps, and spores subsequently adhering to their exoskeletons, led to the hypothesis that termites disperse G.necrorhizus spores. To test this hypothesis, we used microsatellite markers and population genetics analyses to understand patterns of clonality and population structure of G.necrorhizus. While Armillaria individuals can spread vegetatively over large areas, high genotypic diversity in G.necrorhizus populations suggests spores are the primary mode of dispersal. Spatial genetic structure analyses show that G.necrorhizus sporocarps within 238m of each other are more closely related than would be expected by chance and conservative estimates from population assignment tests suggest gene flow no longer occurs between sporocarps separated by 2km. These distances are consistent with previous studies analysing foraging distances of the termites found associated with G.necrorhizus sporocarps. Termites have rarely been recorded to specifically target fungal sporocarps, making this a potentially novel fungal-insect interaction.

ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms

Abstract Understanding how landscape features affect functional connectivity among populations is a cornerstone of spatial ecology and landscape genetic analyses. However, parameterization of resistance surfaces that best describe connectivity is a challenging and often subjective process. ResistanceGA is an R package that utilizes a genetic algorithm to optimize resistance surfaces based on pairwise genetic data and effective distances calculated using CIRCUITSCAPE, least cost paths or random‐walk commute times. Functions in this package allow for the optimization of categorical and continuous resistance surfaces, and simultaneous optimization of multiple resistance surfaces. ResistanceGA provides a coherent framework to optimize resistance surfaces without a priori assumptions, conduct model selection, and make inference about the contribution of each surface to total resistance. ResistanceGA fills a void in the landscape genetic toolbox, allowing for unbiased optimization of resistance surfaces and for the simultaneous optimization of multiple resistance surfaces to create novel composite resistance surfaces, but could have broader applicability to other fields of spatial ecological research.

Development of microsatellite loci for Cryptocarya mandioccana Meisner (Lauraceae) and their genotyping success in different tissues

ABSTRACT Nine polymorphic microsatellite loci were isolated and characterized for Cryptocarya mandioccana Meisner, a tree from the Atlantic Rainforest with seeds dispersed by large animals. The loci were characterized using 48 individuals from two populations and their genotyping success tested in four tissues: leaves from adults and seedlings, and two diaspore maternal tissues. Maternity analyses were also performed on diaspores and leaves from nine adult trees. The number of alleles per locus ranged from nine to 15 and the observed and expected heterozygosities ranged from 0.214 to 0.864 and 0.745 to 0.892, respectively. The loci genotyping success did not significantly differ between tissues and varied from 56 to 96%. The microsatellites showed enough polymorphism to assign the nine adult trees to their diaspores. The successful genotyping in all tissues and identification of mother trees show that the microsatellites are suitable for studies such as spatial genetic structure and maternity analyses.

Population genetic analysis reveals barriers and corridors for gene flow within and among riparian populations of a rare plant.

Landscape features and life-history traits affect gene flow, migration and drift to impact on spatial genetic structure of species. Understanding this is important for managing genetic diversity of threatened species. This study assessed the spatial genetic structure of the rare riparian Grevillea sp. Cooljarloo (Proteaceae), which is restricted to a 20 km2 region impacted by mining in the northern sandplains of the Southwest Australian Floristic Region, an international biodiversity hotspot. Within creek lines and floodplains, the distribution is largely continuous. Models of dispersal within riparian systems were assessed by spatial genetic analyses including population level partitioning of genetic variation and individual Bayesian clustering. High levels of genetic variation and weak isolation by distance within creek line and floodplain populations suggest large effective population sizes and strong connectivity, with little evidence for unidirectional gene flow as might be expected from hydrochory. Regional clustering of creek line populations and strong divergence among creek line populations suggest substantially lower levels of gene flow among creek lines than within creek lines. There was however a surprising amount of genetic admixture in floodplain populations, which could be explained by irregular flooding and/or movements by highly mobile nectar-feeding bird pollinators. Our results highlight that for conservation of rare riparian species, avoiding an impact to hydrodynamic processes, such as water tables and flooding dynamics, may be just as critical as avoiding direct impacts on the number of plants.

Phylogeography of the sandy beach amphipod Haustorioides japonicus along the Sea of Japan: Paleogeographical signatures of cryptic regional divergences

Recent findings of genetic breaks within apparently continuous marine populations challenge the traditional vicariance paradigm in population genetics. Such “invisible” boundaries are sometimes associated with potential geographic barriers that have forced divergence of an ancestral population, habitat discontinuities, biogeographic disjunctions due to environmental gradients, or a combination of these factors. To explore the factors that influence the genetic population structure of apparently continuous populations along the Sea of Japan, the sandy beach amphipod Haustorioides japonicus was examined. We sampled a total of 300 individuals of H. japonicus from the coast of Japan, and obtained partial sequences of the mitochondrial COI gene. The sequences from 19 local populations were clustered into five groups (Northwestern Pacific, Northern, Central, Southern Sea of Japan, and East China Sea) based on a spatial genetic mixture analysis and a minimum-spanning network. AMOVA and pairwise Fst tests further supported the significant divergence of the five groups. Phylogenetic analysis revealed the relationship among the haplotypes of H. japonicus and outgroups, which inferred the northward range expansion of the species. A relaxed molecular-clock Bayesian analysis inferred the early-to middle-Pleistocene divergence of the populations. Among the five clusters, the Central Sea of Japan showed the highest values for genetic diversity indices indicating the existence of a relatively stable and large population there. The hypothesis is also supported by Bayesian Skyline Plots that showed sudden population expansion for all the clusters except for Central Sea of Japan. The present study shows genetic boundaries between the Sea of Japan and the neighboring seas, probably due to geographic isolation during the Pleistocene glacial periods. We further found divergence between the populations along the apparently continuous coast of the Sea of Japan. Historical changes in the geographic range of H. japonicus in relation to sandy beach habitat availability, account for the genetic breaks among the three populations in the Sea of Japan. The present results infer that the past geographic events influenced the population formation of H. japonicus.

Spatial and Temporal Genetic Analysis of Walleyes in the Ohio River

AbstractPrevious genetic analyses have shown that Walleyes Sander vitreus in the upper Ohio River comprise two distinct genetic strains: (1) fish of Great Lakes origin that were stocked into the Ohio River basin and (2) a remnant native strain (Highlands strain). Resource agencies are developing management strategies to conserve and restore the native strain within the upper reaches of the Ohio River. Hybridization between strains has impacted the genetic integrity of the native strain. To better understand the extent and effects of hybridization on the native strain, we used mitochondrial DNA and microsatellite markers to evaluate the spatial (river sections) and temporal (pre‐ and poststocking) genetic diversity of Ohio River Walleyes. Contemporary Lake Erie Walleyes and archival museum specimens collected from the Ohio River basin were used for comparison to contemporary Ohio River samples. Although there was evidence of hybridization between strains, most of the genetic diversity within the Ohio River was partitioned by basin of origin (Great Lakes versus the Ohio River), with greater similarity among river sections than between strains within the same section. Results also suggested that the native strain has diverged from historical populations. Furthermore, notable decreases in measures of genetic diversity and increased relatedness among native‐strain Walleyes within two sections of the Ohio River may be related to stocking aimed at restoration of the Highlands strain. Our results suggest that although the Highlands strain persists within the Ohio River, it has diverged over time, and managers should consider the potential impacts of future management practices on the genetic diversity of this native strain.

Phylogeography and population differentiation in the Psittacanthus calyculatus (Loranthaceae) mistletoe: a complex scenario of climate–volcanism interaction along the Trans‐Mexican Volcanic Belt

AbstractAimThe formation of the Trans‐Mexican Volcanic Belt (TMVB) played an important role in driving inter‐ and intraspecific diversification at high elevations. However, Pleistocene climate changes and ecological factors might also contribute to plant genetic structuring along the volcanic belt. Here, we analysed phylogeographical patterns of the parrot‐mistletoe Psittacanthus calyculatus to determine the relative contribution of these different factors.LocationTrans‐Mexican Volcanic Belt.MethodsUsing nuclear and chloroplast DNA sequence data for 370 individuals, we investigate the genetic differentiation of 35 populations across the species range. We conducted phylogenetic, population and spatial genetic analyses of P. calyculatus sequences along with ecological niche modelling and Bayesian inference methods to gain insight into the structuring of genetic variation of these populations.ResultsOur analyses revealed population structure with three genetic groups corresponding to individuals from Oaxaca and those from the central‐eastern and western TMVB regions. A significant genetic signal of demographic expansion, an east‐to‐west expansion predicted by species distribution modelling, and approximate Bayesian computation analyses strongly supported a scenario of habitat isolation and invasion of TMVB by P. calyculatus during the late‐Pleistocene.Main conclusionsThe genetic differentiation of P. calyculatus may be explained by the combined effects of (1) geographical isolation linked to the effects of the glacial/interglacial cycles and environmental factors, driving genetic differentiation from congeners into more xeric vegetation and (2) the invasion of TMVB from east to west, suggesting a role for both colonization and glacial/interglacial cycles models.

Phylogeography of the finless porpoise and potential implications for the taxonomy of Neophocaena spp.

The finless porpoise (genus Neophocaena) is a poorly known cetacean of great conservation concern. Within its range, from western Pacific to northwestern Indian Ocean, there are currently two species recognized (N. asiaeorientalis and N. phocaenoides), thought to be reproductively isolated since last glacial maximum, with the only sympatric overlap zone in Taiwan Strait. However, the genetic variation across the genus’ distribution has not yet been extensively studied, especially in the Indian Ocean. We performed an exhaustive review of molecular data of the finless porpoise across its range. Neighbor-net networks analyses based on two mitochondrial loci (control region/CR and cytochrome b/cyt b) suggest that finless porpoises from the Indian and Pacific Ocean constitute two distinct clades, well-defined by fixed mutations at both loci. A molecular clock analyses indicate early split (CR: 13.1 Ma, cyt b: 12.9 Ma) between these two oceanic lineages, while spatial genetic analyses further suggest that in the Pacific the divergence was primarily due to the taxon from Japanese waters rather than inter-species divergence across the Taiwan Strait. As extinction risks can be substantially underestimated if threatened species are pooled together with non-threatened, especially in the absence of long-distance migration, we suggest that the present 2-species taxonomy of the genus Neophocaena should be given further examination, with concerted sampling effort in the Western Indian Ocean. More research effort and genomic information is needed before taxonomic revisions can be considered; such further studies are strongly recommended as they may affect the current status classification of the species constituting the genus Neophocaena. Most notably, the narrow-ridged finless porpoise off Japan merits urgent conservation attention.