Comparative genomics of widespread and narrow-range white-bellied rats in the Niviventer niviventer species complex sheds light on invasive rodent success.

Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation, thus enabling range expansion. In contrast, narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions, thus limiting their ability to expand into novel environments. However, the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood. The Niviventer niviventer species complex (NNSC), consisting of highly abundant wild rats in Southeast Asia and China, offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related. In the present study, we combined ecological niche modeling with phylogenetic analysis, which suggested that sister species cannot be both widespread and dominant within the same geographical region. Moreover, by assessing heterozygosity, linkage disequilibrium decay, and Tajima's D analysis, we found that widespread species exhibited higher genetic diversity than narrow-range species. In addition, by exploring the "genomic islands of speciation", we identified 13 genes in highly divergent regions that were shared by the two widespread species, distinguishing them from their narrow-range counterparts. Functional annotation analysis indicated that these genes are involved in nervous system development and regulation. The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.

Abundance and population growth estimates for bare-nosed wombats.

Wildlife managers often rely on population estimates, but estimates can be challenging to obtain for geographically widespread species. Spotlight surveys provide abundance data for many species and, when conducted over wide spatial scales, have potential to provide population estimates of geographically widespread species. The bare-nosed wombat (Vombatus ursinus) has a broad geographical range and is subject to spotlight surveys. We used 19 years (2002-2020) of annual spotlight surveys to provide the first estimates of population abundance for two of the three extant bare-nosed wombat subspecies: V. u. ursinus on Flinders Island; and V. u. tasmaniensis on the Tasmanian mainland. Using distance sampling methods, we estimated annual rates of change and 2020 population sizes for both subspecies. Tasmanian mainland surveys included habitat data, which allowed us to also look for evidence of habitat associations for V. u. tasmaniensis. The average wombat density estimate was higher on Flinders Island (0.42 ha-1, 95% CI = 0.25-0.79) than on the Tasmanian mainland (0.11 ha-1, CI = 0.07-0.19) and both wombat subspecies increased over the 19-year survey period with an estimated annual growth rate of 2.90% (CI = -1.7 to 7.3) on Flinders Island and 1.20% (CI = -1.1 to 2.9) on mainland Tasmania. Habitat associations for V. u. tasmaniensis were weak, possibly owing to survey design; however, we detected regional variation in density for this subspecies. We estimated the population size of V. u. ursinus to be 71,826 (CI = 43,913-136,761) on Flinders Island, which when combined with a previously published estimate of 2599 (CI = 2254-2858) from Maria Island, where the subspecies was introduced, provides a total population estimate. We also estimated 840,665 (CI = 531,104-1,201,547) V. u. tasmaniensis on mainland Tasmania. These estimates may be conservative, owing to individual heterogeneity in when wombats emerge from burrows. Although these two subspecies are not currently threatened, our population estimates provide an important reference when assessing their population status in the future, and demonstrate how spotlight surveys can be valuable to inform management of geographically widespread species.

Genetic variation and population structure of a widely distributed damselfly (Ischnura senegalensis).

Ischnura senegalensis Rambur, 1842 is among the most widespread damselfly species in the world. Unlike dragonflies with strong migration abilities, I. senegalensis have limited dispersing abilities. Gene flow among I. senegalensis populations may be greatly influenced by anthropogenic disturbance, fragmented suitable habitats, sea straits, or even global warming. In this study, to investigate the genetic diversity of I. senegalensis populations, we sequenced and collected 498 cytochrome oxidase I sequences across the Old World. Haplotype network analysis showed 51 haplotypes and I. senegalensis could be grouped into four regions (Afrotropical region, Oriental region, main Islands of Japan, and the Ryukyu Islands), each of which contains different dominant haplotypes. Based on molecular variance analysis, we found that populations from the Afrotropical region have quite a low gene flow with the Asian populations (except Yemen). Furthermore, rice cultivation may aid the dispersion of I. senegalensis in the oriental region. Populations from the Ryukyu Islands show the highest genetic diversity, which may be due to the geological separation among islands. Our results prove that I. senegalensis has great genetic diversity among different populations across the world.

Phenotypic plasticity masks range-wide genetic differentiation for vegetative but not reproductive traits in a short-lived plant.

Genetic differentiation and phenotypic plasticity jointly shape intraspecific trait variation, but their roles differ among traits. In short-lived plants, reproductive traits may be more genetically determined due to their impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-treatment greenhouse experiment with observational field data throughout the range of a widespread short-lived herb, Plantago lanceolata, we (1) disentangled genetic and plastic responses of functional traits to a set of environmental drivers and (2) assessed how genetic differentiation and plasticity shape observational trait-environment relationships. Reproductive traits showed distinct genetic differentiation that largely determined observational patterns, but only when correcting traits for differences in biomass. Vegetative traits showed higher plasticity and opposite genetic and plastic responses, masking the genetic component underlying field-observed trait variation. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related to fitness.

Genetic differentiation among populations of the blackfin goodea Goodea atripinnis (Cyprinodontiformes: Goodeidae): implications for its evolutionary history.

Central Mexico is characterized by a complex topography that is the result of historic and contemporary tectonic and climatic factors. These events have influenced the evolutionary history of numerous freshwater fishes in the region. Nonetheless, recent studies have shown that life-history traits and ecological characteristics of species may influence dispersal capabilities and the degree of genetic connectivity. Goodea (Cyprinodontiformes: Goodeidae) is one of the most widely distributed and environmentally tolerant genera of goodeids. In this study, the authors analysed variation in the mitochondrial cytochrome b gene to evaluate the phylogeographic relationships, genetic structure, genetic diversity and demographic history of Goodea from across its distribution range. They found low genetic differentiation and identified shared haplotypes among several regions. Geographic segregation was found in samples southwest and northeast of the Lower Lerma region, with some internal isolated groups showing phylogeographic differentiation and unique haplotypes. The AMOVA best explained genetic structure when grouped by haplogroups rather than when grouped by recognized biogeographic regions. Several regions showed null genetic diversity, raising the possibility of dispersal mediated by humans. Finally, Bayesian Skyline Plot analysis showed a population expansion for the Southwest haplogroup, except for the Armería population and sub-group II of the Northeast haplogroup. All this suggests a recent colonization of Goodea atripinnis throughout some of the biogeographic regions currently inhabited by this species.

Effects of climate and geography on spatial patterns of genetic structure in tropical skinks.

Knowledge of how contemporary and historical factors drive patterns of genetic structure across geographic space can shed light on the processes underlying diversification. This approach is especially fruitful in studies of widespread species or species clades that occur across multiple environmental conditions and biomes. In the Neotropics, specifically, molecular data from widespread vertebrate species have revealed high levels of lineage diversity and spatial genetic structure - yet studies that explore the possible correlates of local structure patterns are lacking. We investigate the distribution of lineage diversity within two widespread South American skink species complexes of the genus Mabuya. We characterize genetic structure and diversity in these widely ranged lizards, and identify potential geographic and environmental correlates, to shed light on the processes that promote lineage diversification across the heterogeneous landscapes which they occupy. In both groups, we found mitochondrial lineages to be spatially structured along the coastal forests and the savannas of Brazil. These mtDNA patterns are, however, not shared with those inferred from nuclear DNA markers. The geographic location of major mitochondrial genetic breaks is consistent with those of other taxa, suggesting common responses to former landscape change in eastern South America, particularly along geological faults. Genetic differentiation is correlated with environmental turnover and geographic separation in one, but not in the other, group of skinks. Compared to other studies of similarly widely distributed organisms, the link between spatial environmental gradients and genetic differentiation is not as strong or consistent, suggesting a more complex history underlying current phylogeographic patterns. Our genetic data indicate the existence of yet undescribed diversity in wide-ranging lizards, and the value of phylogenetic and phylogeographic studies of similarly understudied species.

The complete mitochondrial genome of Orthonychiurus folsomi (Collembola: Onychiuridae).

The complete mitochondrial genome of Orthonychiurus folsomi (Schäffer 1900) was sequenced, assembled, and annotated. The mitochondrial genome of O. folsomi has a length of 15,283bp and comprises 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. Two tRNA genes trnS(uga) and trnQ have changed position. A phylogenetic tree of Onychiuridae species showed the polyphyly of this family.

Cryptic Diversity in the Widespread Asian Ant Crematogaster rothneyi (Hymenoptera: Formicidae) Inferred from Morphological and Genetic Evidence.

The myrmicine species Crematogaster rothneyi is one of the most widely distributed ants in Asia, but it has rarely been collected in the field. Its distribution range covers South and Southeast Asia, extending approximately 5,000 km from India in the west to Sulawesi in the east. Despite this wide distribution range, C. rothneyi has been treated as a single taxonomic species, and no combined morphological or molecular analysis has been conducted to assess whether any intraspecific variation exists. The sequence divergences of C. rothneyi populations, mainly obtained from Southeast Asia, were investigated by analyzing 387 bp and 175 bp sequences of the 12S ribosomal RNA and cytochrome c oxidase subunit (COI) genes, respectively. Phylogenetic analysis indicated that the C. rothneyi populations were separated into three groups: group I from Thailand and Cambodia, group II from Bangladesh and Myanmar, and group III from Krakatau and Sulawesi. Groups II and III were recovered as a single clade, sister to group I. The interspecific divergences were 7.3% to 8.5% for 12S and 14.5% to 23.3% for COI between most C. rothneyi specimens and Cambodian specimens, while divergence for 12S was 3.5% between Thai and Cambodian specimens. The Thai specimens are not morphologically differentiated, and are considered conspecific to C. rothneyi. We describe the Cambodian series as a new species, Crematogaster yaharai sp. nov., based on unique antennal morphology and mesosomal sculpture patterns with molecular evidence. Crematogaster rothneyi civa Forel, 1902 is synonymized under C. rothneyi. Crematogaster rothneyi is widespread and has sister species, suggesting recent diversification within the Indochinese Peninsula.

Geographic variation of Moenkhausia bonita (Characiformes: Characidae) in the rio de la Plata basin, with distributional comments on M. intermedia

Moenkhausia bonita occurs in numerous additional localities from the Bermejo, Paraná, Paraguay, and Uruguay river basins. Given that this finding greatly expands the distributional range of M. bonita, we carried out an intraspecific comparison, using multivariate methods for 18 morphometric and eight meristic characters taken from a comprehensive sample of 536 specimens. All localities were distributed in four major geographic groups as follows: Bermejo, Paraná, Paraguay, and Uruguay. Results of the morphometric comparisons showed significant differences among the studied groups except between the Paraguay and Uruguay groups. Statistical differences in meristic values were found for most between-group comparisons, especially in those resulting from discriminant canonical analyses (DCA). Specimens from the Bermejo basin were the most distinct group in most morphological comparisons. However, the overall subtle differences found in body morphology likely reflect intraspecific variation within M. bonita and seem to be mainly influenced by spatial and environmental features of drainages. As M. bonita was previously identified as M. intermedia in the río de La Plata basin, distributional comments on the latter species in that basin are provided.(AU)

Moenkhausia bonita es registrada en numerosas localidades adicionales de las cuencas de los ríos Bermejo, Paraná, Paraguay, y Uruguay. Dado que estos hallazgos expanden ampliamente el rango distribucional de M. bonita, nosotros llevamos a cabo una comparación intraespecífica, usando métodos multivariados para 18 características morfométricas y 8 merísticas que fueron tomados en una muestra exhaustiva de 536 especímenes. Todas las localidades fueron repartidas en cuatro grupos principales como sigue: Bermejo, Paraná, Paraguay y Uruguay. Los resultados de las comparaciones morfométricas mostraron diferencias significativas a través de los grupos bajo estudio, excepto entre los grupos Paraguay y Uruguay. Diferencias estadísticas fueron encontrados en la mayoría de las comparaciones entre los grupos, especialmente en aquellas obtenidas de los análisis discriminantes canónicos (ADC). Los especímenes de la cuenca del Bermejo fueron encontrados como el grupo más divergente en la mayoría de las comparaciones morfológicas. No obstante, estas leves diferencias encontradas en la morfología del cuerpo son consideradas dentro de la variación intraespecífica de M. bonita y parecen estar influidas por características ambientales y espaciales de los drenajes. Dado que M. bonita fue previamente identificada como M. intermedia en la cuenca del río de La Plata, comentarios distribucionales sobre esta última especie en esta cuenca son presentados.(AU)

Testing the niche-breadth-range-size hypothesis: habitat specialization vs. performance in Australian alpine daisies.

Relatively common species within a clade are expected to perform well across a wider range of conditions than their rarer relatives, yet experimental tests of this "niche-breadth-range-size" hypothesis remain surprisingly scarce. Rarity may arise due to trade-offs between specialization and performance across a wide range of environments. Here we use common garden and reciprocal transplant experiments to test the niche-breadth-range-size hypothesis, focusing on four common and three rare endemic alpine daisies (Brachyscome spp.) from the Australian Alps. We used three experimental contexts: (1) alpine reciprocal seedling experiment, a test of seedling survival and growth in three alpine habitat types differing in environmental quality and species diversity; (2) warm environment common garden, a test of whether common daisy species have higher growth rates and phenotypic plasticity, assessed in a common garden in a warmer climate and run simultaneously with experiment 1; and (3) alpine reciprocal seed experiment, a test of seed germination capacity and viability in the same three alpine habitat types as in experiment 1. In the alpine reciprocal seedling experiment, survival of all species was highest in the open heathland habitat where overall plant diversity is high, suggesting a general, positive response to a relatively productive, low-stress environment. We found only partial support for higher survival of rare species in their habitats of origin. In the warm environment common garden, three common daisies exhibited greater growth and biomass than two rare species, but the other rare species performed as well as the common species. In the alpine reciprocal seed experiment, common daisies exhibited higher germination across most habitats, but rare species maintained a higher proportion of viable seed in all conditions, suggesting different life history strategies. These results indicate that some but not all rare, alpine endemics exhibit stress tolerance at the cost of reduced growth rates in low-stress environments compared to common species. Finally, these findings suggest the seed stage is important in the persistence of rare species, and they provide only weak support at the seedling stage for the niche-breadth-range-size hypothesis.

Taxonomic revision of Galeocharax (Characiformes: Characidae: Characinae)

The taxonomy of Galeocharax, a genus of freshwater fishes distributed in most South American cis-Andean river systems, except the rio Negro, rio São Francisco and rio Xingu basins and the eastern drainages of Brazil, is herein revised. A total of 1229 specimens were examined from which 680 had meristic and morphometric data taken. Osteological and morphological features were also examined through radiographs, scanning electron microscopy and in cleared and stained specimens. Three of the four species previously considered as valid are herein recognized: Galeocharax humeralis from rio Paraguay and lower rio Paraná basins; Galeocharax goeldii, from rio Madeira basin, with records of geographical distribution expanded to the río Madre de Dios, río Beni, rio Mamoré and rio Guaporé basins and Galeocharax gulo, which is widespread throughout rio Amazonas, río Orinoco, rio Tocantins, and upper rio Paraná basins. Galeocharax knerii is herein considered a junior synonym of Galeocharax gulo. A key to species of Galeocharax is presented.(AU)

A taxonomia de Galeocharax, um gênero de peixes de água doce distribuído nos principais sistemas hídricos da América do Sul cisandina, com exceção da bacia do rio Negro, do rio São Francisco, do rio Xingu e das drenagens litorâneas do leste, é aqui revisada. Foram examinados 1229 exemplares, dos quais 680 tiveram dados merísticos e morfométricos tomados. Características osteológicas e morfológicas também foram examinadas por meio de radiografias, microscopia eletrônica de varredura e exemplares diafanizados. Três das quatro espécies previamente consideradas válidas são reconhecidas: Galeocharax humeralis das bacias do rio Paraguai e baixo rio Paraná; Galeocharax goeldii da bacia do rio Madeira, com registros de distribuição geográfica ampliados para as bacias dos rios Madre de Dios, Beni, Mamoré e Guaporé, e Galeocharax gulo amplamente distribuída nas bacias dos rios Amazonas, Orinoco, Tocantins e alto rio Paraná. Galeocharax knerii foi considerada sinônimo júnior de Galeocharax gulo. Uma chave de identificação para as espécies de Galeocharax é apresentada.(AU)

A revision of the "African Non-Spiny" Clade of Solanum L. (Solanum sections Afrosolanum Bitter, Benderianum Bitter, Lemurisolanum Bitter, Lyciosolanum Bitter, Macronesiotes Bitter, and Quadrangulare Bitter: Solanaceae).

The African Non-Spiny (ANS) clade contains 14 species of mostly large canopy lianas or scandent shrubs confined to Madagascar (10) and continental Africa (4, with with one species reaching the southern Arabian peninsula). Members of the clade were previously classified in sections Afrosolanum Bitter, Benderianum Bitter, Lemurisolanum Bitter, Macronesiotes Bitter and Quadrangulare Bitter, and were throught to be related to a variety of New World groups. The group is an early-branching lineage of non-spiny solanums and characters shared with other vining New World solanums are homoplastic. The 14 species of the group occupy a wide range of habitats, from wet forests in western Africa to savanna and dry forests of southern Madagascar and dune habitats in South Africa. Many members of the group are highly variable morphologically, and habit can vary between shrub and canopy vine in a single locality. We here review the taxonomic history, morphology, potential relationships and ecology of these species; we provide keys for their identification, descriptions, full synonymy (including designations of lectotypes and neotypes) and nomenclatural notes. Illustrations, distribution maps and preliminary conservation assessments are provided for all species.

Biogeography of "Cyprinella lutrensis": intensive genetic sampling from the Pecos River 'melting pot' reveals a dynamic history and phylogenetic complexity.

Thorough sampling is necessary to delineate lineage diversity for polytypic "species" such as Cyprinella lutrensis. We conducted extensive mtDNA sampling (cytochrome b and ND4) from the Pecos River, Rio Grande, and South Canadian River, New Mexico. Our study emphasized the Pecos River due to its complex geological history and potential to harbor multiple lineages. We used geometric-morphometric, morphometric, and meristic analyses to test for phenotypic divergence and combined nucDNA with mtDNA to test for cytonuclear disequilibrium and combined our sequences with published data to conduct a phylogenetic re-assessment of the entire C. lutrensis clade. We detected five co-occurring mtDNA lineages in the Pecos River, but no evidence for cytonuclear disequilibrium or phenotypic divergence. Recognized species were interspersed amongst divergent lineages of "C. lutrensis". Allopatric divergence among drainages isolated in the Late Miocene and Pliocene apparently produced several recognized species and major divisions within "C. lutrensis". Pleistocene re-expansion and subsequent re-fragmentation of a centralized lineage founded younger, divergent lineages throughout the Rio Grande basin and Edwards Plateau. There is also evidence of recent introductions to the Rio Grande, Pecos and South Canadian Rivers. Nonetheless, deeply divergent lineages have coexisted since the Pleistocene.

Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates.

Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.

Revision of sternaspis otto, 1821 (polychaeta, sternaspidae).

To the memory of William Ronald Sendall Sternaspid polychaetes are common and often abundant in soft bottoms in the world oceans. Some authors suggest that only one species should be recognized, whereas others regard a few species as widely distributed in many seas and variable depths from the low intertidal to about 4400 m. There are some problems with species delineation and the distinctive ventro-caudal shield has been disregarded or barely used for identifying species. In order to clarify these issues, the ventral shield is evaluated in specimens from the same locality and its diagnostic potential is confirmed. On this basis, a revision of Sternaspis Otto, 1821 (Polychaeta: Sternaspidae) is presented based upon type materials, or material collected from type localities. The sternaspid body, introvert hooks and shield show three distinct patterns, two genera have seven abdominal segments and tapered introvert hooks, and one genus has eight abdominal segments and spatulate introvert hooks. The ventro-caudal shield has three different patterns: stiff with ribs, and sometimes concentric lines, stiff with feebly-defined ribs but no concentric lines, and soft with firmly adhered sediment particles. Sternaspis is restricted to include species with seven abdominal segments, falcate introvert hooks, and stiff shields, often exhibiting radial ribs, concentric lines or both. Sternaspis includes, besides the type species, Sternaspis thalassemoides Otto, 1821 from the Mediterranean Sea, Sternaspis affinis Stimpson, 1864 from the Northeastern Pacific, Sternaspis africana Augener, 1918, stat. n. from Western Africa, Sternaspis andamanensis sp. n. from the Andaman Sea, Sternaspis costata von Marenzeller, 1879 from Japan, Sternaspis fossor Stimpson, 1853 from the Northwestern Atlantic, Sternaspis islandica Malmgren, 1867 from Iceland, Sternaspis maior Chamberlin, 1919 from the Gulf of California, Sternaspis princeps Selenka, 1885 from New Zealand, Sternaspis rietschi Caullery, 1944 from abyssal depths around Indonesia, Sternaspis scutata (Ranzani, 1817) from the Mediterranean Sea, Sternaspis spinosa Sluiter, 1882 from Indonesia, and Sternaspis thorsoni sp. n. from the Iranian Gulf. Two genera are newly proposed to incorporate the remaining species: Caulleryaspis and Petersenaspis. Caulleryaspis gen. n. is defined by the presence of falcate introvert hooks, seven abdominal segments, and soft shields with sediment particles firmly adhered on them; it includes two species: Caulleryaspis gudmundssoni sp. n. from Iceland and Caulleryaspis laevis (Caullery, 1944) comb. n. from Indonesia. Petersenaspis gen. n. is defined by the presence of spatulate introvert hooks, eight abdominal segments, and stiff shields with poorly defined ribs but no concentric line; it includes Petersenaspis capillata (Nonato, 1966) from Brazil and Petersenaspis palpallatoci sp. n. from the Philippines. Neotypes are proposed for eight species: Sternaspis thalassemoides, Sternaspis affinis, Sternaspis africana, Sternaspis costata, Sternaspis fossor, Sternaspis maior, Sternaspis scutata and Sternaspis spinosa, to stabilize these species-group names, and a lectotype is designated for Sternaspis laevis which is transferred to Caulleryaspis gen. n. The geographic range of most species appears to be much smaller than previously indicated, and for some species additional material in good condition is needed to clarify their distributions. Keys to genera and to all species are also included.