Effects of errors in range maps on estimates of historical species richness of mammals in Canadian national parks

Aim Tests for faunal relaxation in reserves, particularly for mammals, have relied on comparisons of current species richness with estimates of species richness derived from historical range maps. However, any range map reflects the extent of occurrence of species and not necessarily the area of occupancy. Thus, estimates of historical species richness might be prone to error introduced by ‘false positives’, that is, a species might be considered to have been present in locations where it actually was not. The effect of such ‘false positives’ could bias statistical tests of faunal relaxation to type I error, and result in estimates of the extent of faunal relaxation in reserves greater than was actually the case. We evaluated the potential for errors in historical range maps to generate inflated estimates of historical species richness of mammals at sites that are reserves today. Location Canadian national parks in the Canadian portion of the Alleghenian‐‐Illinoian mammal province in south‐eastern Canada (the maritime region and parts of southern Québec, Ontario and Manitoba). Methods The effect of varying levels of error in range maps on estimates of historical species richness was tested using geographical information systems (GIS)‐based statistical sampling of simulated historical ranges. Species’ areas of occupancy were simulated to be only 25%, 75% and 95% of published historical species ranges. For each reserve, estimates of historical species richness from these simulated species ranges were then compared with similar, previously published estimates of richness based on published historical species ranges. Results Previous estimates of historical species richness for reserves were inversely and linearly related to the degree of inaccuracy of species ranges. If species ranges were, on average, 5% smaller than the accepted ranges, then estimates of historical species richness agreed with previous estimates in c. 90% of cases. However, if historical ranges were, on average, 25% smaller than those used in previous analyses, then previous historical estimates of species richness may be overestimates in c. 40% of cases. Main conclusions Estimates of the extent of faunal relaxation in reserves that use historical range maps to quantify past species richness appear to be sensitive to even small errors in the degree to which range maps may overestimate ‘area of occupancy’.     

Freakish patterns – species and species concepts in apomicts

Apomict groups keep challenging taxonomists, in classifications as well as in more fundamental question about the nature of apomictic species. The latter question is not just an academic one, because the outcome influences practical decisions on biodiversity and conservation. A historical overview over the species problem shows that a period of confusion and proliferation of species concepts between 1940 and 1990 was followed by an increasing consensus at the end of the 20th century that the species category is heterogeneous. Species come in kinds, which is understandable in light of their different evolutional histories. Recently, Wilkins stated that we do not need a generally applicable species concept, because species are not an a priori category into which all biological organisms must fit, but salient phenomena that are to be explained. Not only biparental, but also asexual organisms often form such species‐as‐phenomena, explained as some combination of adaptation to an ecological niche and reproductive compatibility. The above is illustrated by historical and current studies in three well‐studied apomict groups, viz. Ranunculus cassubicus agg., Rubus subgen. Rubus and Hieracium (subgen. Hieracium and Pilosella). Species in the Ranunculus cassubicus aggregate are the few existing sexuals, which are surrounded by a hybrid swarm of only partial apomictic forms, whereas in Rubus subgen. Rubus and Hieracium s.s. sexuals as well as numerous apomicts form well defined species. How species should be circumscribed in Pilosella is yet to be clarified. Largely, the differences between these groups can be contributed to their different modes of apomixis and the associated retained sexuality. From this review it is clear that the question is not so much ‘What is a species?‘, but ‘What is a species in this particular group?‘ To answer this question a thorough knowledge and understanding of the biology of the genus in question is required.     

Comparative biogeography reveals differences in population genetic structure of five species of stream fishes

The distribution of genetic variation in Texas stream fishes has been shaped by a complex mix of historical and anthropogenic factors. Although Texas was not glaciated during the Pleistocene, the rise in sea level following this epoch isolated formerly connected drainages. More recently, the construction of dams, modifications of stream systems, and the release of commercially raised fish have influenced the patterns of genetic diversity. To examine how these different factors have impacted Texas stream fishes, we compared the genetic structure of five species of fish spanning two families and inhabiting two adjacent drainages: Lepomis megalotis, Lepomis cyanellus, Cyprinella lutrensis, Cyprinella venusta, and Campostoma anomalum. Our analyses of the mitochondrial D‐Loop show that genetic patterns differ strongly across species. A phylogeographical split between the Brazos and Trinity drainages was seen in conspecific populations of Lepomis species and is probably the result of the historical separation of these river systems. In contrast, contemporary ecological and anthropogenic factors, such as the desiccation of streams during summer, and the translocation of bait fish, appear to have a stronger influence on the genetic patterns in the remaining species. The contrasting results demonstrate the importance of using a multi‐species, comparative approach for landscape genetic studies as single species patterns may not be representative of others and thus may obscure differential effects of historical versus recent events as well as natural versus anthropogenic forces. By comparing closely related species that differ in their life history and economic importance it may be possible to disentangle the relative roles of historical, intrinsic, and anthropogenic influences on different organisms within a region. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Phylogenetic patterns and conservation among North American members of the genus <Emphasis Type="Italic">Agalinis</Emphasis> (Orobanchaceae)

Background  

North American Agalinis Raf. species represent a taxonomically challenging group and there have been extensive historical revisions at the species, section, and subsection levels of classification. The genus contains many rare species, including the federally listed endangered species Agalinis acuta. In addition to evaluating the degree to which historical classifications at the section and subsection levels are supported by molecular data sampled from 79 individuals representing 29 Agalinis species, we assessed the monophyly of 27 species by sampling multiple individuals representing different populations of those species. Twenty-one of these species are of conservation concern in at least some part of their range.     

On the importance of patch attributes, environmental factors and past human impacts as determinants of perennial plant species richness and diversity in Mediterranean semiarid steppes

Richness and diversity of perennial plant species were evaluated in 17 Stipa tenacissima steppes along a degradation gradient in semiarid SE Spain. The main objective of the study was to evaluate the relative importance of historical human impacts, small‐scale patch attributes and environmental factors as determinants of perennial plant species richness and diversity in S. tenacissima steppes, where vegetation is arranged as discrete plant patches inserted on a bare ground matrix. Partial least squares regression was used to determine the amount of variation in species richness and diversity that could be significantly explained by historical human impacts, patch attributes, and environmental factors together and separately. They explained up to 89% and 69% of the variation in species richness and diversity, respectively. In both cases, the predictive power of patch attributes models was higher than that of models consisting of abiotic characteristics and variables related to human impact, suggesting that patch attributes are the major determinants of species richness and diversity in semiarid S. tenacissima steppes. However, patch attributes alone are not enough to explain the observed variation in species richness and diversity. The area covered by late‐successional sprouting shrubs and the distance between consecutive patches were the most influencing individual variables on species richness and diversity, respectively. The implications of these results for the management of S. tenacissima steppes are discussed.     

Evaluating Sierra Nevada Yellow-Legged Frog Distribution Using Environmental DNA

Genetic tools that identify species from trace DNA samples could supplement traditional survey methods to clarify distributional limits of rare species. For species with legal habitat protection, elevational limits of distributions are used to determine where management actions may affect endangered species. The endangered Sierra Nevada yellow-legged frog (Rana sierrae) generally is found down to 1,370 m, but in the Plumas National Forest, California, USA, there are a number of historical records below this elevation, resulting in protections extending to 1,067 m. This species is phenotypically similar to the foothill yellow-legged frog (R. boylii), with which it occasionally hybridizes. We used a combination of genetic methods to investigate the fine-scale distribution of the Sierra Nevada yellow-legged frog in the Plumas National Forest. We collected and analyzed environmental DNA (eDNA) samples from all accessible lower elevation sites with records of Sierra Nevada yellow-legged frog (n = 17) and swabbed 220 individuals for genetic identification from 2016–2018 to clarify the distribution of this endangered species. We created a climatic suitability model using the validated Sierra Nevada yellow-legged frog records and current (1970–2000) climate models to assess additional highly suitable localities for Sierra Nevada yellow-legged frog presence using eDNA capture. We did not confirm detection of Sierra Nevada yellow-legged frog eDNA at any historical sites and identified all swabbed individuals from below 1,370 m (n = 144) as foothill yellow-legged frogs. We located a new Sierra Nevada yellow-legged frog site (at 1,919 m) during surveys guided by the climatic suitability model. It does not appear after extensive eDNA and genetic sampling that the Sierra Nevada yellow-legged frog occurs below 1,370 m in this portion of their range at present. Our results show that eDNA sampling can be used as an effective management tool to evaluate historical locations and previously unknown suitable localities for current presence of a species of interest. © 2021 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.     

Effects of historical forest contraction on the phylogeographic structure of Australo‐Papuan populations of the red‐legged pademelon (Macropodidae: Thylogale stigmatica)

Geographic patterns of genetic variation are strongly influenced by historical changes in species habitats. Whether such patterns are common to co‐distributed taxa may depend on the extent to which species vary in ecology and vagility. We investigated whether broad‐scale phylogeographic patterns common to a number of small‐bodied vertebrate and invertebrate species in eastern Australian forests were reflected in the population genetic structure of an Australo‐Papuan forest marsupial, the red‐legged pademelon (Macropodidae: Thylogale stigmatica). Strong genetic structuring of mtDNA haplotypes indicated the persistence of T. stigmatica populations across eastern Australia and southern New Guinea in Pleistocene refugial areas consistent with those inferred from studies of smaller, poorly dispersing species. However, there was limited divergence of haplotypes across two known historical barriers in the northeastern Wet Tropics (Black Mountain Barrier) and coastal mideastern Queensland (Burdekin Gap) regions. Lack of divergence across these barriers may reflect post‐glacial recolonization of forests from a large, central refugium in the Wet Tropics. Additionally, genetic structure is not consistent with the present delimitation of subspecies T. s. wilcoxi and T. s. stigmatica across the Burdekin Gap. Instead, the genetic division occurs further to the south in mideastern Queensland. Thus, while larger‐bodied marsupials such as T. stigmatica did persist in Pleistocene refugia common to a number of other forest‐restricted species, species‐specific local extinction and recolonization events have resulted in cryptic patterns of genetic variation. Our study demonstrates the importance of understanding individualistic responses to historical climate change in order to adequately conserve genetic diversity and the evolutionary potential of species.     

Seventy years of changes in the abundance of Danish charophytes

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<Emphasis Type="Italic">Maggengo</Emphasis> meadow patches enclosed by forests in the Italian Alps: evidence of landscape legacy on plant diversity

The maggenghi are mid slope meadows typical of all the southern and of great parts of the northern European Alps, for centuries managed with traditional and low intensity techniques. Usually, they are scattered patches in surrounding forests. The spontaneous expansion of trees and shrubs, favored by the recent decline of mountain agriculture, lead the maggengo patches patterns and shapes to change. Our objective was to analyze the effect of this change on current plant diversity of the remnant patches, as the adaptive response could be slow and possibly related more to historical than to current landscape patterns. We analyzed the trend of the size, shape, elongation, fractal dimension and connectivity of maggengo patches of a Central-Eastern Italian Alpine district, in four time steps, from 1973 to 2006, and in 1859, when mountain agriculture was still widespread. Then, we studied the relationships between those landscape metrics and two current patch-level plant diversity measures: interior species richness and species density. Aerial photographs were used to investigate that trend, while a historical cadastral map was used to assess the landscape metrics in 1859. As expected, in the last 30 years, the total size of maggenghi has been reduced by 57% while their shapes have been progressively simplified. Interior species richness was positively related to size, both in 2006 and over the past 30 years, but not to any 1859 measures. Conversely, species density was positively correlated only with 1859 size, shape index and connectivity. We conclude that the historical shape, size and connectivity are some of the key variables affecting the plant species density of maggengo patches, but not of their interior plant species richness.     

Ecological niche conservation and differentiation in the wood-feeding cockroaches, Cryptocercus, in the United States

The distribution of a species is determined by a set of ecological correlates (biotic and abiotic factors) and historical phenomena that define and constrain its ecological niche. By examining the geographical projection of the ecological niche, it is possible to identify areas that are suitable for the species ecologically but that are not actually inhabited. Previous studies have used such discords to anticipate the existence of undescribed species; the absence of species may also result from historical barriers that have prevented colonization of the area. Thus, discords between potential and realized niches of a species may result from aspects of the species’s biology (e.g. lack of dispersal ability, specific habitat requirements) or from barriers to dispersal. In this study, we developed ecological niche models of the five Nearctic species of wood‐feeding cockroaches in the genus Cryptocercus. One species, C. clevelandi, occurs in the western USA and four (C. darwini, C. garciai, C. punctulatus, C. wrighti) are distributed in the Appalachian Mountains in the eastern USA. In general, modelled niches for all species showed ecological restriction relative to the total range of available conditions. Niche models for the eastern USA species predicted the geographical distributions of the other eastern USA species, with the exception of C. garciai, suggesting general overall conservatism in ecological characteristics. Some interspecific differences in modelled niches were also apparent. In general, C. clevelandi was predicted to occupy cooler and drier areas relative to the eastern USA species; among the eastern USA species, C. darwini and C. garciai were predicted to inhabit warmer areas relative to C. punctulatus and C. wrighti. Interspecific differences and similarities were consistent with the phylogenetic relationships among Cryptocercus species previously reported. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90 , 457–466.     

High mitochondrial diversity in geographically widespread butterflies of Madagascar: A test of the DNA barcoding approach

The standardized use of mitochondrial cytochrome c oxidase subunit I (COI) gene sequences as DNA barcodes has been widely promoted as a high-throughput method for species identification and discovery. Species delimitation has been based on the following criteria: (1) monophyletic association and less frequently (2) a minimum 10× greater divergence between than within species. Divergence estimates, however, can be inflated if sister species pairs are not included and the geographic extent of variation within any given taxon is not sampled comprehensively. This paper addresses both potential biases in DNA divergence estimation by sampling range-wide variation in several morphologically distinct, endemic butterfly species in the genus Heteropsis, some of which are sister taxa. We also explored the extent to which mitochondrial DNA from the barcode region can be used to assess the effects of historical rainforest fragmentation by comparing genetic variation across Heteropsis populations with an unrelated forest-associated taxon Saribia tepahi. Unexpectedly, generalized primers led to the inadvertent amplification of the endosymbiont Wolbachia, undermining the use of universal primers and necessitating the design of genus-specific COI primers alongside a Wolbachia-specific PCR assay. Regardless of the high intra-specific genetic variation observed, most species satisfy DNA barcoding criteria and can be differentiated in the nuclear phylogeny. Nevertheless, two morphologically distinguishable candidate species fail to satisfy the barcoding 10× genetic distance criterion, underlining the difficulties of applying a standard distance threshold to species delimitation. Phylogeographic analysis of COI data suggests that forest fragmentation may have played an important role in the recent evolutionary diversification of these butterflies. Further work on other Malagasy taxa using both mitochondrial and nuclear data will provide better insight into the role of historical habitat fragmentation in species diversification and may potentially contribute to the identification of priority areas for conservation.     

Using community and population approaches to understand how contemporary and historical factors have shaped species distribution in river ecosystems

Aim To examine how the employment of both community‐ and population‐level approaches can provide a wider view of the importance of contemporary and historical factors on current species distribution. We posit that community ecology should provide more information about contemporary factors, whereas population genetics should provide better information about historical factors. Location Rivers of the western Mediterranean Basin, including four subregions differing in geological history: the Iberian Plate, Transitional, Betic and Rif. Methods For a community‐level approach, Trichoptera richness and community composition were compared between subregions using species accumulation curves and a correspondence analysis. For a population‐level approach, the mtDNA cytochrome C oxidase subunit I (COI) gene of specimens of the Trichoptera midstream‐lowland species Chimarra marginata (L.) was sequenced and analysed using phylogeographical methods. Results The community approach revealed that historical events had more influence on headwater communities than contemporary ecological factors, whereas historical events had negligible influence on midstream‐lowland communities. In midstream‐lowland sites, however, the population approach showed that the genetic structure of C. marginata differed significantly between subregions and revealed patterns of historical gene migration. In terms of species richness, the Rif subregion had the lowest value per basin due to local climatic features and isolation. Main conclusions Both community‐ and population‐level approaches yielded information about the effects of historical factors on species distribution. However, the importance of historical events on current Trichoptera communities depends on the river zonation. Unlike headwater sites, midstream‐lowland sites showed signs of historical events at the population level but not at the community level at the scale used, indicating that both approaches should be employed together in biogeographical studies. Lack of detection of historical events at the community level does not necessarily mean that they are negligible. Most likely, the organizational level used is not appropriate. We also stress the importance of implementing conservation measures for rivers in the western Mediterranean, especially under future scenarios of climate change and human disturbances in the Mediterranean Basin.     

Phylogenetic systematics and evolution of Agnotecous in New Caledonia (Orthoptera: Grylloidea, Eneopteridae)

Abstract. Within a framework for historical analysis of Eneopterinae biogeography the New Caledonian endemic cricket genus Agnotecous Saussure, 1878 is revised: the eight already known species are diagnosed and six new species described, A. azurensis Desutter‐Grandcolas sp.n. , A. chopardi Desutter‐Grandcolas sp.n. , A. clarus Desutter‐Grandcolas sp.n. , A. doensis Desutter‐Grandcolas sp.n. , A. meridionalis Desutter‐Grandcolas sp.n. and A. occidentalis Desutter‐Grandcolas sp.n. Four species groups are characterized by male genitalic structures. Identification keys are provided for both males and females. A cladistic analysis was performed using fifty‐eight morphological characters. The two resultant topologies, which differ only in topology of three apical species, support the monophyly of Agnotecous and that of the four species groups. Preliminary hypotheses of Eneopterinae historical biogeography are derived from phylogenetic and distributional data.     

Pushing north one bottleneck at a time: site frequency spectra tell the history of Sitka spruce

Reconstructing the history of populations is a longstanding goal of molecular ecologists. In addition to a better understanding of the past, it is hoped that this knowledge would also facilitate predictions regarding species’ responses to future events such as climate change. The traditional way of doing this is through the fossil record, but these historical records are often incomplete. Inferring historical demography from patterns of nucleotide variability can help to fill these gaps. In this issue of Molecular Ecology, Holliday et al. (2010) glimpse into the demographic past of Sitka spruce, Picea sitchensis, an economically and ecologically important species native to northwestern United States and Canada, by examining the site frequency spectrum (SFS) of 153 loci in six populations covering the species entire range.     

Lack of phylogeographic structure in three widespread Australian birds reinforces emerging challenges in Australian historical biogeography

Aims Building on molecular studies of widespread Australian vertebrates, we tested whether each of three widespread Australian bird species, namely the singing honeyeater, Lichenostomus virescens, spiny‐cheeked honeyeater, Acanthagenys rufogularis (Passeriformes: Meliphagidae), and black‐faced woodswallow, Artamus cinereus (Passeriformes: Artamidae), has undergone a recent (Pleistocene) range expansion across the Australian continent. We related the findings to the presence or absence of geographic variation in each species’ external phenotype and whether historical or non‐historical factors have been involved in generating variation. Methods A total of 92 specimens of the three species were collected from, as far as possible, the same localities across Australia. They were sampled for mitochondrial DNA (mtDNA) diversity in the 1041 base pairs of the ND2 gene, and these data were analysed with nucleotide diversity statistics, unrooted networks, nested clade analysis, and tests of range expansion or stability. Results Range expansions could not be rejected in any of the species in our study. Each had low, geographically unstructured nucleotide diversity. Patterns of geographic variation in the singing honeyeater's and, to a lesser extent, the black‐faced woodswallow's external phenotypes are not correlated with mtDNA diversity in ND2. Main conclusions Our study adds to the increasing number of data sets suggesting the apparent prevalence of Pleistocene population expansions in widespread Australian birds. Furthermore, it shows that observable geographic structure may evolve very quickly, in response either to environmental gradients or to historical factors that operated too recently to be detected by ND2 sequences (e.g. in the singing honeyeater). Conversely, we have shown that a species that has had a recent population expansion need not necessarily be geographically invariant. To understand fully the interplay between vicariance and dispersal in the history of widespread Australian arid‐zone birds, or between the historical and non‐historical origins of their differentiation, carefully conducted case‐by‐case molecular studies will be necessary. Only then will biogeographical patterns and the processes that led to them emerge. Study of the historical biogeography and the more recent population history of Australian arid‐zone birds has reached a point where mtDNA‐based studies, while still informative and contributing to a growing data base of such work, should be complemented with data from multiple, rapidly evolving nuclear loci.     

Phylogenetics,historical biogeography and molecular species delimitation of Gnaptorina Reitter (Coleoptera: Tenebrionidae: Blaptini)

With 38 described species or subspecies, Gnaptorina Reitter is the second‐most species‐rich genus in the darkling beetle subtribe Gnaptorinina (Tenebrionidae: Tenebrioninae). In this study, we reconstructed a phylogeny of the genus based on one nuclear and three mitochondrial genes and used this phylogeny to explore the historical biography and diversification of Gnaptorina species. We implemented multiple molecular species delimitation approaches to reassess the status of Gnaptorina species and taxonomic subdivisions of the genus. Dating and historical biogeography analyses suggest an early Eocene origin of the genus, with the southeastern regions of the Tibetan Plateau most likely as areas of origin. Based on these results, we propose a new classification for Gnaptorina with three major clades identified. Consequently, the monotypic subgenus Boreoptorina is newly synonymized with the more species‐rich subgenus Hesperoptorina, and G. dongdashanensis Shi is transferred from Hesperoptorina to the subgenus Gnaptorina. In addition, G. minxiana Medvedev, formerly treated as a subspecies of G. potanini Reitter, is elevated to species. Results of molecular species delimitation analyses are largely congruent and confirm the status of most morphological species.     

Ulva (Chlorophyta,Ulvales) Biodiversity in the North Adriatic Sea (Mediterranean,Italy): Cryptic Species and New Introductions

Ulva Linnaeus (Ulvophyceae, Ulvales) is a genus of green algae widespread in different aquatic environments. Members of this genus show a very simple morphology and a certain degree of phenotypic plasticity, heavily influenced by environmental conditions, making difficult the delineation of species by morphological features alone. Most studies dealing with Ulva biodiversity in Mediterranean waters have been based only on morphological characters and a modern taxonomic revision of this genus in the Mediterranean is not available. We report here the results of an investigation on the diversity of Ulva in the North Adriatic Sea based on molecular analyses. Collections from three areas, two of which subject to intense shipping traffic, were examined, as well as historical collections of Ulva stored in the Herbarium Patavinum of the University of Padova, Italy. Molecular analyses based on partial sequences of the rbcL and tufA genes revealed the presence of six different species, often with overlapping morphologies: U. californica Wille, U. flexuosa Wulfen, U. rigida C. Agardh, U. compressa Linnaeus, U. pertusa Kjellman, and one probable new taxon. U. californica is a new record for the Mediterranean and U. pertusa is a new record for the Adriatic. Partial sequences obtained from historical collections show that most of the old specimens are referable to U. rigida. No specimens referable to the two alien species were found among the old herbarium specimens. The results indicate that the number of introduced seaweed species and their impact on Mediterranean communities have been underestimated, due to the difficulties in species identification of morphologically simple taxa as Ulva.