Genetic structure among populations in the endemic Hawaiian Plantago lineage: insights from microsatellite variation

Endemic Hawaiian species in the genus Plantago show considerable morphological and ecological diversity. Despite their variation, a recent phylogenetic analysis based on DNA sequence data showed that the group is monophyletic and that sequence variation among species and morphotypes is low. This lack of sequence polymorphisms resulted in an inability to resolve species and population affinities within the most recently derived clade of this lineage. To assess species boundaries, population genetic structure and interpopulation connectivity among the morphologically and ecologically distinct populations within this clade, genetic variation was examined using eight microsatellite loci. Within‐population genetic diversity was found to be lowest in the Maunaiu, Hawai'i population of the endangered P. hawaiensis, and highest in the large P. pachyphylla population from 'Eke, West Maui. Isolation by distance across the range of populations was detected and indicated restricted dispersal. This result is likely to be attributable to few interisland dispersal events in the evolutionary history of this lineage. Genetic differentiation within islands tended to be higher among populations occurring in contrasting bog and woodland habitats, suggesting ecological barriers to gene flow and the potential role of ecological divergence in population diversification. Overall, these results are consistent with findings from phylogenetic analysis of the entire lineage. Our data bring new insights regarding patterns of dispersal and population genetic structure to this endemic and endangered group of island taxa. As island environments become increasingly fragmented, information of this type has important implications for the successful management of these fragile populations and habitats.     

Investigating niche and lineage diversification in widely distributed taxa: phylogeography and ecological niche modeling of the Peromyscus maniculatus species group

The relationship between lineage formation and variation in the ecological niche is a fundamental evolutionary question. Two prevailing hypotheses reflect this relationship: niche conservatism and niche divergence. Niche conservatism predicts a pattern where sister taxa will occupy similar niche spaces; whereas niche divergence predicts that sister taxa will occupy different niche spaces. Widely distributed species often show distinct phylogeographic structure, but little research has been conducted on how the environment may be related to these phylogenetic patterns. We investigated the relationship between lineage divergence and environmental space for the closely related species Peromyscus maniculatus and P. polionotus utilizing phylogenetic techniques and ecological niche modeling (ENM). We estimated the phylogenetic relationship among individuals based on complete cytochrome b sequences that represent individuals from a majority of the species ranges. Niche spaces that lineages occupy were estimated by using 12 environmental layers. Differences in niche space were tested using multivariate statistics based on location data, and ENMs were employed using maximum entropy algorithms. Two similarity indices estimated significant divergence in environmental space based on the ENM. Six geographically structured lineages were identified within P. maniculatus. Nested within P. maniculatus we found that P. polionotus recently diverged from a clade occupying central and western United States. We estimated that the majority of the genetic lineages occupy distinct environmental niches, which supports a pattern of niche divergence. Two sister taxa showed niche divergence and represent different ecomorphs, suggesting morphological, genetic and ecological divergence between the two lineages. Two other sister taxa were observed in the same environmental space based on multivariate statistics, suggesting niche conservatism. Overall our results indicate that a widely distributed species may exhibit both niche conservatism and niche divergence, and that most lineages seem to occupy distinct environmental niches.     

At least some meiofaunal species are not everywhere. Indication of geographic,ecological and geological barriers affecting the dispersion of species of Ototyphlonemertes (Nemertea,Hoplonemertea)

Most meiofaunal species are known to have a broad distribution with no apparent barriers to their dispersion. However, different morphological and/or molecular methods supported patterns of diversity and distribution that may be different among taxa while also conflicting within the same group. We accurately assessed the patterns of geographic distribution in actual genetic species of a marine meiofaunal animal model: Ototyphlonemertes. Specimens were collected from several sites around Europe, Northern and Central America, Southern America, Pacific Islands and Asia. We sequenced regions of two mitochondrial and two nuclear genes. Using single‐gene, a concatenated data set, multilocus approaches and different DNA taxonomy methods, we disentangled the actual diversity and the spatial structures of haplotypes and tested the possible correlation between genetic diversity and geographic distance. The results show (i) the importance of using several genes to uncover both diversity and highlight phylogeographic relationships among species and that (ii) independent genetic evolutionary entities have a narrower distribution than morphological species. Moreover, (iii) a Mantel test supported a positive correlation between genetic and geographical distance. By sampling from the two sides of Isthmus of Panama, we were additionally able to identify lineage divergence times that are concordant with vicariance mechanisms caused by the geological closure of the seaway across the Isthmus. We therefore propose that in addition to distance, other geological and ecological conditions are also barriers to the dispersion of and gene flow in marine meiofaunal organisms.     

Morphological and niche divergence of pinyon pines

The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation.     

Molecular systematics and biodiversity of the Cryptotis mexicanus group (Eulipotyphla: Soricidae): two new species from Honduras supported

Small-eared shrews of the genus Cryptotis (Mammalia: Eulipotyphla: Soricidae) are widespread in the northern Neotropics. Systematic studies of these shrews over the past two decades have revealed previously undocumented morphological and species diversity, resulting in a quadrupling of the number of recognized species. Unfortunately, a small proportion of the species in the genus have been included in molecular phylogenetic studies, and evolutionary relationships within the genus are incompletely known. Traditionally, species have been assigned to four or five morphologically defined ‘species groups’, but tests of the monophyly of some of these groups show weak support and relationships amongst species groups remain somewhat speculative. The largest species group is the C. mexicanus group inhabiting Mexico and northern Central America. We studied sequences from mitochondrial cytochrome-b and 16S genes, as well as nuclear ApoB and BRCA1 genes from 22 species of Cryptotis, including 15 species in the C. mexicanus group. Our combined analysis shows that the C. goldmani subgroup is very weakly supported as monophyletic; however, the C. mexicanus group as a whole is not monophyletic. Our molecular phylogenetic analyses confirm the distinctiveness of two newly described species (C. celaque and C. mccarthyi) from isolated highlands of western Honduras and illustrate their relationship with other species formerly considered part of a widespread C. goodwini.     

A new species of small-eared shrew in the <Emphasis Type="Italic">Cryptotis thomasi</Emphasis> species group from Costa Rica (Mammalia: Eulipotyphla: Soricidae)

We describe a new species of small-eared shrew, genus Cryptotis Pomel, 1848 (Eulipotyphla: Soricidae), from near the community of Monteverde in the Tilarán highlands of northwestern Costa Rica. The new species is immediately distinguished from all other Costa Rican shrews its large size and long tail. Morphologically, it belongs to the Cryptotis thomasi group of small-eared shrews, a clade that is more typically distributed in the Andes Cordillera and other highland regions of northern South America. The new Costa Rican species and the Panamanian endemic Cryptotis endersi Setzer, 1950 are the only two members of this species group known to occur in Central America. Like most other members of the C. thomasi group for which the postcranial skeleton has been studied, the new species tends be more ambulatory (rather than semi-fossorial) when compared with other members of the genus. Our survey efforts over several decades failed to locate a population of the new species, and we discuss its conservation status in light of its limited potential distribution in the Tilarán highlands and the significant climatic change that has been documented in the Monteverde region during the past four decades.     

Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil‐calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron region of nitrate reductase (NIA‐i3) to examine genetic diversity within species, rates of gene flow among species and ancestral population size of disjunct sister species. Transitions in functional and morphological traits associated with ecological and climatic niche axes were examined across the phylogeny. We found the Virentes to be monophyletic with three subclades, including a southwest clade, a southeastern US clade and a Central American/Cuban clade. Despite high leaf morphological variation within species and transpecific chloroplast haplotypes, RADseq and nuclear SSR data showed genetic coherence of species. We estimated a crown date for Virentes of 11 Ma and implicated the formation of the Sea of Cortés in a speciation event ~5 Ma. Tree height at maturity, associated with fire tolerance, differs among the sympatric species, while freezing tolerance appears to have diverged repeatedly across the tropical–temperate divide. Sympatric species thus show evidence of ecological niche differentiation but share climatic niches, while allopatric and parapatric species conserve ecological niches, but diverge in climatic niches. The mode of speciation and/or degree of co‐occurrence may thus influence which niche axis plants diverge along.     

Mitochondrial diversification of the Peromyscus mexicanus species group in Nuclear Central America: biogeographic and taxonomic implications

The mountain mice of the Peromyscus mexicanus group currently encompass six known species; however, the limits between species remain uncertain, with two considered monotypic and the other four having multiple associated subspecific names. Based on the most comprehensive sampling of the group throughout its distribution in Nuclear Central America, we used data of the mitochondrial cytochrome b gene to assess its genetic diversity, phylogeny, and main biogeographic and diversification patterns. Our mitochondrial phylogeny only partially reflects the current taxonomy of the group, in agreement with some of the taxonomically recognized species. Specifically, our phylogenetic results show that the group is highly structured, including four main clades with genetic distances ranging from 11 to 8.6%. A remarkable level of differentiation is found at a more local level, defined as 15 different lineages with high nucleotide and haplotype diversity (π = 0.068, h = 0.99), and with divergence and genetic distance values (p‐uncorrected = 9.9–2.4%; K2P = 10.8–3.0%) similar to values observed between species within Peromyscus. Accordingly, we propose that the reference name P. mexicanus is polyphyletic and should be restricted to the mountains of central Mexico west of the Isthmus of Tehuantepec. We suggest to limit the other five recognized specific names to equal number of lineages, as monophyletic, and to revalidate three junior synonyms: Peromyscus salvadorensis, P. nicaraguae and P. tropicalis. The Isthmus of Tehuantepec, the Motagua‐Polochic‐Jocotán fault system, the Maya Highlands and the Honduras Depression are examples of geographic features that are likely associated with the differentiation of main lineages. Some other lineages may represent candidate species, hence the need to review the taxonomic status of the entire P. mexicanus group.     

Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists

Aim To evaluate the role of historical processes in the evolution of Sclerurus leaftossers by integrating phylogenetic and phylogeographical approaches. Location Humid forests of the Neotropical region. Methods We reconstructed the evolutionary history of Sclerurus based on DNA sequences representing all species and 20 of the 26 recognized subspecies using one autosomal nuclear locus and three protein‐coding mitochondrial gene sequences. Phylogenetic relationships were inferred using Bayesian and maximum‐likelihood methods. We used Bayesian coalescent‐based approaches to evaluate demographic changes through time, and to estimate the timing of diversification events. Based on these results, we examined the temporal accumulation of divergence events using lineage‐through‐time plots. Results The monophyly of all Sclerurus species was strongly supported except for Sclerurus mexicanus, which was paraphyletic in relation to Sclerurus rufigularis, and for the sister pair Sclerurus scansor–Sclerurus albigularis, which were not reciprocally monophyletic in the nuclear tree. We found remarkably deep phylogeographical structure within all Sclerurus species, and overall this structure was congruent with currently recognized subspecies and Neotropical areas of endemism. Diversification within Sclerurus has occurred at a relatively constant rate since the Middle Miocene. Main conclusions Our results strongly support the relevance of physiographical (e.g. Nicaragua Depression, Isthmus of Panama, Andean Cordillera, great rivers of Amazonia) and ecological barriers (open vegetation corridor) and ecological gradients (elevational zonation) to the diversification of Neotropical forest‐dwelling organisms. Despite the high congruence among the spatial patterns identified, the variance in divergence times suggests multiple speciation events occurring independently across the same barrier, and a role for dispersal. The phylogenetic patterns and cryptic diversity uncovered in this study demonstrate that the current taxonomy of Sclerurus underestimates the number of species.     

Lack of congruence of genetic and niche divergence in Podarcis hispanicus complex

Niche divergence among closely related lineages can be informative on the ecological and evolutionary processes involved in differentiation, particularly in the case of cryptic species complexes. Here we compared phylogenetic relationships and niche similarity between pairs of lineages included in the Podarcis hispanicus complex to examine patterns of niche divergence and its role in the organization of current diversity patterns, as allopatric, parapatric, and sympatric lineages occur in the Western Mediterranean Basin. First, we used ecological niche models to characterize the realized climatic niche of each Podarcis hispanicus complex lineage based on topographic and climatic variables, to identify important variables, and to test for niche conservatism or divergence between pairs of lineages. Variables related to precipitation generally exhibited the highest contribution to niche models, highlighting the importance of rainfall levels in shaping distributions of Podarcis wall lizards. We found that most forms have significant differences in realized climatic niches that do not follow the pattern of mitochondrial divergence. These results lend support to the hypothesis that genetic divergence across Podarcis hispanicus complex most likely occurred in allopatric conditions, mostly with significant niche divergence. Competition after secondary contact is also suggested by the common occurrence of niche overlap between lineages that exhibit strictly parapatric distribution. The almost continuous distribution of Podarcis lizards in the study area appears to be a result of a combination of complementary suitable niches and competition, which seem two important mechanisms limiting geographic distributions and restricting the existence of extensive contact zones.     

Phylogeography of the bark beetle Dendroctonus mexicanus Hopkins (Coleoptera: Curculionidae: Scolytinae)

Dendroctonus mexicanus is polyphagous within the Pinus genus and has a wide geographical distribution in Mexico and Guatemala. We examined the pattern of genetic variation across the range of this species to explore its demographic history and its phylogeographic pattern. Analysis of the mtDNA sequences of 173 individuals from 25 Mexican populations allowed to us identify 53 geographically structured haplotypes. High haplotype and low nucleotide diversities and Tajima’s D indicate that D. mexicanus experienced rapid population expansion during its dispersal across mountain systems within its current range. The nested clade phylogeographic analysis indicates that the phylogeographic pattern of D. mexicanus is explained by continuous dispersion among lineages from the Sierra Madre Occidental, the Sierra Madre Oriental and the Trans-Mexican Volcanic Belt. However, we also observed isolation events among haplotypes from the Cofre de Perote/Trans-Mexican Volcanic Belt/Sierra Madre Oriental and the Trans-Mexican Volcanic Belt/Sierra Madre del Sur, which is consistent with the present conformation of mountain systems in Mexico and the emergence of geographical barriers during the Pleistocene.     

Cryptic niche conservatism among evolutionary lineages of an invasive lizard

Aim There is increasing evidence that the quality and breadth of ecological niches vary among individuals, populations, evolutionary lineages and therefore also across the range of a species. Sufficient knowledge about niche divergence among clades might thus be crucial for predicting the invasion potential of species. We tested for the first time whether evolutionary lineages of an invasive species vary in their climate niches and invasive potential. Furthermore, we tested whether lineage‐specific models show a better performance than combined models. Location Europe. Methods We used species distribution models (SDMs) based on climatic information at native and invasive ranges to test for intra‐specific niche divergence among mitochondrial DNA (mtDNA) clades of the invasive wall lizard Podarcis muralis. Using DNA barcoding, we assigned 77 invasive populations in Central Europe to eight geographically distinct evolutionary lineages. Niche similarity among lineages was assessed and the predictive power of a combination of clade‐specific SDMs was compared with a combined SDM using the pooled records of all lineages. Results We recorded eight different invasive mtDNA clades in Central Europe. The analysed clades had rather similar realized niches in their native and invasive ranges, whereas inter‐clade niche differentiation was comparatively strong. However, we found only a weak correlation between geographic origin (i.e. mtDNA clade) and invasive occurrences. Clades with narrow realized niches still became successful invaders far outside their native range, most probably due to broader fundamental niches. The combined model using data for all invasive lineages achieved a much better prediction of the invasive potential. Conclusions Our results indicate that the observed niche differentiation among evolutionary lineages is mainly driven by niche realization and not by differences in the fundamental niches. Such cryptic niche conservatism might hamper the success of clade‐specific niche modelling. Cryptic niche conservatism may in general explain the invasion success of species in areas with apparently unsuitable climate.     

Testing the role of climate in speciation: New methods and applications to squamate reptiles (lizards and snakes)

Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large‐scale phylogeny to identify 242 sister species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n = 49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61–76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms.     

Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias)

The importance of the environment in shaping phenotypic evolution lies at the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus Neotamias) are part of a very recent radiation, occupying a wide range of environments with marked niche partitioning among species. One open question is if and how those differences in environments affected phenotypic evolution in this lineage. Herein we examine the relative importance of genetic drift versus natural selection in the origin of cranial diversity exhibited by clade members. We also explore the degree to which variation in potential selective agents (environmental variables) are correlated with the patterns of morphological variation presented. We found that genetic drift cannot explain morphological diversification in the group, thus supporting the potential role of natural selection as the predominant evolutionary force during Neotamias cranial diversification, although the strength of selection varied greatly among species. This morphological diversification, in turn, was correlated with environmental conditions, suggesting a possible causal relationship. These results underscore that extant Neotamias represent a radiation in which aspects of the environment might have acted as the selective force driving species’ divergence.     

Ecological niche comparison and molecular phylogeny segregate the invasive moss species Campylopus introflexus (Leucobryaceae,Bryophyta) from its closest relatives

The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer, has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus. Analyses of an extended ITS dataset displayed statistically supported incongruence between ITS1 and ITS2. ITS1 separates the New World clade of C. pilifer from a clade comprising C. introflexus and the Old World C. pilifer. Ancestral state reconstruction showed that this topology is morphologically supported by differences in the height of the dorsal costal lamellae in leaf cross‐section (despite some overlap). ITS2, in contrast, supports the current morphological species concept, i.e., separating C. introflexus from C. pilifer, which is morphologically supported by the orientation of the hyaline hair point at leaf apex as well as costal lamellae height. Re‐analysis of published and newly generated plastid atpB‐rbcL spacer sequences supported the three ITS lineages. Ecological niche modeling proved a useful approach and showed that all three molecular lineages occupy distinct environmental spaces that are similar, but undoubtedly not equivalent. In line with the ITS1 topology, the C. pilifer lineage from the New World occupies the most distinct environmental niche, whereas the niches of Old World C. pilifer and C. introflexus are very similar. Taking the inferences from ecological niche comparisons, phylogenetics, and morphology together, we conclude that all three molecular lineages represent different taxa that should be recognized as independent species, viz. C. introflexus, C. pilifer (Old World clade), and the reinstated C. lamellatus Mont. (New World clade).     

地理因素对箭竹复合体遗传多样性与遗传分化的影响

地理因素对植物天然居群的物种分布和种内分化具有重要影响。该研究通过对箭竹复合体内39个居群的14对SSR数据进行深入分析,旨在揭示重要地理因素(如海拔、纬度、地理距离)对该复合体内遗传多样性和遗传分化式样的影响。结果表明:(1)糙花箭竹亚支系遗传多样性最高(H_e=0.50),而团竹亚支系的遗传多样性最低(H_e=0.33)。(2)遗传多样性与纬度、海拔在A、B两个支系水平呈显著正相关关系,但在亚支系水平,遗传多样性的变化趋势呈现出更为复杂的局面,部分支系表现为负相关关系,推测纬度和海拔对箭竹复合体内遗传多样性水平具有一定影响,但也需重视其他进化因素的作用。(3)Mantel检验显示,仅在团竹亚支系中检测出较弱的正相关关系,表明地理距离不是影响箭竹复合体内遗传分化的主导因素,后续需结合基因流检测推断杂交事件对其遗传分化的影响。     

Phylogeny and Niche Conservatism in North and Central American Triatomine Bugs (Hemiptera: Reduviidae: Triatominae), Vectors of Chagas' Disease

The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios.     

The diversification of the genus Monodelphis and the chronology of Didelphidae (Didelphimorphia)

To evaluate the monophyletic status of the genus Monodelphis, and its species complexes, we used a 9.3‐kb multimarker alignment to build a phylogenetic tree based on the largest taxon sampling for this didelphid genus to date. Furthermore, using a Bayesian framework and six calibration points, we inferred the divergence times for the major Monodelphis lineages and their current geographical distribution to perform an ancestral state reconstruction for geographical areas. Our results indicate the monophyletic nature of Monodelphis and suggest ‘kunsi’ as a new species complex that includes Monodelphis kunsi and an undescribed species. Monodelphis is further subdivided into three clades showing a common vicariance pattern, with each major clade consisting of a northern South American lineage joined with an Atlantic Forest lineage. This geographic consistency suggests a vicariant event that might have been related to a warm period at the Oligocene/Miocene border, according to our time results. © 2015 The Linnean Society of London