Niche Modelling Analyses Research Articles

Adaptation to different temperatures results in wing size divergence of the invading species Drosophila nasuta (Diptera: Drosophilidae) in Brazil.

Invasive species threaten biodiversity on a global scale. The success of invasions depends on the species' adaptation to the different environmental conditions of new territories. Studies show that invasive insects present evolutionary changes in wing morphology in areas they are introduced to in response to abiotic conditions. In the last decade, the Asian Drosophila nasuta fly invaded and spread widely throughout Brazil. This insect has preferences for conserved environments and is related to the likely reduction in the abundance of native drosophilids in the Atlantic Forest. Ecological niche modelling analyses showed that rainfall and temperature are the main factors which delimit the geographic distribution of this species. Herein, we verified the existence of significant differences in the wing sizes of D. nasuta in Brazil and evaluated the influence of abiotic factors (rainfall and temperature) on the observed patterns. We conducted 11 measurements on the right-side wings of 240 D. nasuta males collected in the Amazon Forest, Caatinga, Cerrado and Atlantic Forest. Statistical analyses revealed the existence of two groups: one with larger wings, which brought together samples from locations with the lowest temperatures; and one with smaller wings, which corresponded to places with a hotter climate. One explanation for this result is the fact that large wings favour greater heat capture by flies in colder climates, increasing their survival chances in these environments. These rapid evolutionary changes in D. nasuta in this first decade of invasion in Brazil reveal the enormous adaptive potential of this species in this megadiverse country.

Phylogeography and population genomics of the critically endangered aquatic plant Caldesia grandis in China

Caldesia grandis, a critically endangered aquatic species, is predominantly found in the mid-low mountainous swamps of subtropical China. This study assessed the genetic diversity and population structure of the species using RAD-seq data, explored its phylogeography across the extant nine populations based on five plastid DNA (ptDNA) regions, and conducted niche modeling analysis. We found low genetic diversity (HE = 0.180, Ho = 0.222, and π = 0.197) and genetic differentiation among populations (Fst = 0.089), which was likely due to genetic drift in small populations and frequent inter-population contact during the Quaternary period. Although RAD-seq analysis did not reveal a clear population structure, two distinct clades, comprising western and eastern populations, were identified using five ptDNA haplotypes. Molecular dating and niche modeling suggested that the uplift of the Luoxiao Mts may have contributed to the divergence of the eastern and western clades (ca. 1.51 Ma)during the Pleistocene, which also supports the hypothesis that the Nanling Mts acted as a refugium for C. grandis. Additionally, the repeated glacial periods of the Quaternary, accompanied by contraction and expansion of suitable habitats, likely facilitated gene exchange among populations, influencing the current distribution pattern in subtropical China. Our results suggested that each ptDNA haplotype should be treated as an independent unit for conservation purposes, and ex-situ efforts should be prioritized to conserve C. grandis in China.

Phylogeny, niche modelling and morphology unveil a new lianescent species of Sigmoidotropis (Leguminosae, Papilionoideae) across rainforest enclaves within Brazilian dry vegetation

AbstractThe small Neotropical papilionoid legume genus Sigmoidotropis (nine species) has been described only relatively recently as the result of the taxonomic rearrangement of the genus Vigna (subtribe Phaseolinae), based on phylogenetic analyses of DNA sequence data. Here, we formally propose a new lianescent species of Sigmoidotropis that occurs disjunctly in enclaves of moist forest of mountainous regions surrounded by dry vegetation at three different localities in the Brazilian states of Bahia and Minas Gerais. Its phylogenetic position and morphological affinities with other genera of Phaseolinae were evaluated by Bayesian inference and maximum likelihood analyses, using sequence data from the nuclear ITS/5.8S and plastid trnK/matK. To better understand this new species’ widely disjunct distribution and a possible connection between its populations in the past, an environmental niche modelling (ENM) analysis was performed. The phylogenetic analyses revealed that Sigmoidotropis appears closest to the genera Ancistrotropis and Delgadoana, together forming the Sigmoid‐keel clade. The new species proposed here is strongly recovered within Sigmoidotropis, being most closely related to S. ekmaniana, S. elegans, and S. megatyla. The ENM indicated changes in the potential distribution of the new species over different climatic periods, with expansion during colder periods and contraction during warmer periods, leading to possible relictual populations in moist forest enclaves. A description of the new species Sigmoidotropis maculata is presented, along with illustrations, a distribution map, taxonomic comments, and conservation status assessment.

The use of ecological niche models improves biogeographic regionalization of the Balsas Depression, Mexico

AbstractAimBiogeographic regionalization classifies zones in terms of their biotas and contributes to understanding the ecological and historical factors that affect the distribution of species. We use Ecological Niche Modeling (ENM) to complement missing information on species distribution and thus improve the accuracy of biogeographic boundaries.LocationBalsas Depression Floristic Province, Mexico.MethodsBased on parameters documented in herbarium collections and environmental variables, ENM was carried out to determine the most suitable environmental conditions for a species to thrive (i.e., the species' ecological niche). The ENM and spatial analysis were used to obtain the biogeographic regionalization of the seasonally dry tropical forest (SDTF) in the Balsas Depression (BD), Mexico, through spatial analysis. Using the Maxent algorithm, we constructed ecological niche models (ENMs) of 134 flowering plant species distributed preferentially in the SDTF (characteristic species), most of them endemic to the BD. Subsequently, we obtained an incidence matrix based on the information from the 134 ENMs, which was used to analyze the turnover of species in Biodiverse software. The turnover matrix was used for Non‐metric Multidimensional Scaling (NMDS) ordination and clustering analyses. Finally, the environmental predictors most related to species turnover were identified using the relative environmental turnover method.ResultsThe clustering analysis divided the SDTF in the BD into four floristic districts — two located in its western part and two in the eastern region. The NMDS differentiated, in the first component, two districts in the western region and one in the eastern. Seven environmental variables contributed significantly to explaining the turnover of species in these districts; the most significant were the elevation, pH, and precipitation of the coldest quarter.Main ConclusionsThe use of ENM for the regionalization of areas with high species richness allows for a more detailed classification of subregions and the distribution patterns of the species that define their limits. This provides a more solid theoretical basis for the investigation of biogeographic patterns.

Historical Demography and Climate Driven Range Shifts in the Blue-spotted Salamander Under the Climate Change Scenarios

This study integrates phylogeography with distributional analysis to understand the demographic history and range dynamics of a limited dispersal capacity amphibian species, Blue-spotted Salamander (Ambystoma laterale), under several climate change scenarios. For this we used an ecological niche modeling approach, together with Bayesian based demographic analysis, to develop inferences regarding this species' demographic history and range dynamics. The current model output was mostly congruent with the present distribution of the Blue-spotted Salamander. However, under both the Last Interglacial and the Last Glacial Maximum bioclimatic conditions, the model predicted a substantially narrower distribution than the present. These predictions showed almost no suitable area in the current distribution range of the species during almost the last 22.000 y before present (ybp). The predictions indicated that the distribution of this species shifted from eastern coast of northern North America to the southern part of the current distribution range of the species. The Bayesian Skyline Plot analysis, which provided good resolution of the effective population size changes over the Blue-spotted Salamander history, was mostly congruent with ecological niche modeling predictions for this species. This study provides the first investigation of the Blue-spotted Salamander’s late-Quaternary history based on ecological niche modeling and Bayesian-based demographic analysis. In terms of the main result of this study, we found that the species' present genetic structure has been substantially affected by past climate changes, and this species has reached current distribution range almost from nothing since the Last Glacial Maximum.

Ecological niche modeling analysis (Cx. pipiens), potential risk and projection of Dirofilaria spp. infection in Greece

Vector-borne diseases continue to increase worldwide. Dirofilariosis is one of the most common vector-borne zoonotic diseases, mainly caused by Dirofilaria spp. (D. immitis and D. repens) and spread by culicid mosquitoes of different species. Greece is one of the countries in southern Europe where it is traditionally endemic, and its distribution is not homogeneous. The aim of this study was to develop an environmental model for Greece that reflects the suitability of the ecological niche for Dirofilaria spp. infection risk and its projection until 2080. For this purpose, we used the potential distribution of suitable habitats for Culex pipiens calculated using an ecological niche model (ENM) and the potential number of generations of Dirofilaria spp. The ecological niche model of Cx. pipiens in Greece showed good predictive power (AUC=0.897) with the parasite at a resolution of 1 km2. The variables that contributed most to the model were mean annual temperature, rivers and human footprint. The highest risk of infection was found in coastal areas and in riverside areas of the main river basins, as well as in irrigated areas of the mainland and peninsular regions and in the whole territory of island areas, and the lowest risk was found in areas of higher altitude. A positive relationship was found between the risk of dirofilariosis and the location of infected dogs, with 86.65% located in very high and high risk areas. In 2080, the percentage of territory gained by Cx. pipiens will increase by 261.52%. This model provides a high predictive value, predicted presence, and risk of Dirofilaria spp. infection and can serve as a tool for the management and control of this disease.

Tracing histoplasmosis genomic epidemiology and species occurrence across the USA

ABSTRACT Histoplasmosis is an endemic mycosis in North America frequently reported along the Ohio and Mississippi River Valleys, although autochthonous cases occur in non-endemic areas. In the United States, the disease is provoked by two genetically distinct clades of Histoplasma capsulatum sensu lato, Histoplasma mississippiense (Nam1) and H. ohiense (Nam2). To bridge the molecular epidemiological gap, we genotyped 93 Histoplasma isolates (62 novel genomes) including clinical, environmental, and veterinarian samples from a broader geographical range by whole-genome sequencing, followed by evolutionary and species niche modelling analyses. We show that histoplasmosis is caused by two major lineages, H. ohiense and H. mississippiense; with sporadic cases caused by H. suramericanum in California and Texas. While H. ohiense is prevalent in eastern states, H. mississipiense was found to be prevalent in the central and western portions of the United States, but also geographically overlapping in some areas suggesting that these species might co-occur. Species Niche Modelling revealed that H. ohiense thrives in places with warmer and drier conditions, while H. mississippiense is endemic to areas with cooler temperatures and more precipitation. In addition, we predicted multiple areas of secondary contact zones where the two species co-occur, potentially facilitating gene exchange and hybridization. This study provides the most comprehensive understanding of the genomic epidemiology of histoplasmosis in the USA and lays a blueprint for the study of invasive fungal diseases.

Interspecific niche overlap and climatic associations of native Quercus species in the Zagros forests of Iran

In the arid regions surrounding southwestern Asia, oak trees play an important role in the environment by conserving water and preserving soil and supporting wildlife. There are concerns for the health and continued productivity of these forests, and there is a widespread oak decline. In this study, ecological niche modeling (ENM) and multivariate principal component analysis (PCA) were used to determine the environmental variations among Quercus brantii, Q. infectoria, and Q. libani in the Zagros forests of western Iran. Based on the area under the curve (AUC > 0.9) and the true skill statistic (TSS > 0.8), three algorithms, including random forest (RF), maximum entropy (MaxEnt), and maximum picking neural net (MAXnet), were used in an ensemble approach to explore the most important environmental variables within the projected suitable habitat of each species. Environmental variables related to climate, including annual precipitation (bio12) and annual mean temperature (bio1), were among the most important drivers of habitat suitability for oak species. The results illustrated that suitable areas for Q. infectoria and Q. libani often occur in the northern parts of the Zagros, which are humid and cooler than the southern areas. The results suggested that Q. brantii has a higher tolerance for harsh conditions in Zagros and therefore inhabits almost all areas of Zagros, including the southern parts. The climatic overlap between pairs of species was found to be significant based on equivalency and similarity tests, suggesting that the environmental conditions of the two species compared are more similar than would be expected by chance. The gap analysis for the three oak species revealed that only a few protected areas currently exist within their suitable habitats, with most of the highly suitable habitats located on non-protected lands, particularly for Q. libani and Q. infectoria. In addition, deforestation is known to sometimes occur within the boundaries of protected areas. Improving the level of protection by upgrading the current protected areas to national parks can help with conservation.

Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes.

Numerous studies have revealed that past geological events and climatic fluctuations had profoundly affected the genetic structure and demographic patterns of species. However, related species with overlapping ranges may have responded to such environmental changes in different ways. In this study, we compared the genetic structure and population dynamics of two typical desert shrubs with overlapping distributions in northern China, Nitraria tangutorum and Nitraria sphaerocarpa, based on chloroplast DNA (cpDNA) variations and species distribution models. We sequenced two cpDNA fragments (trnH-trnA and atpH-atpI) in 633 individuals sampled from 52 natural populations. Twenty-four chlorotypes, including eight rare chlorotypes, were identified, and a single dominant haplotype (H4) widely occurred in the entire geographical ranges of the two species. There were also a few distinctive chlorotypes fixed in different geographical regions. Population structure analyses suggested that the two species had significantly different levels of total genetic diversity and interpopulation differentiation, which was highly likely correlated with the special habitat preferences of the two species. A clear phylogeographic structure was identified to exist among populations of N. sphaerocarpa, but not exist for N. tangutorum. The neutral tests, together with the distribution of pairwise differences revealed that N. tangutorum experienced a sudden demographic expansion, and its expansion approximately occurred between 21 and 7 Kya before present, while a rapid range expansion was not identified for N. sphaerocarpa. The ecological niche modeling (ENM) analysis indicated that the potential ranges of two species apparently fluctuated during the past and present periods, with obvious contraction in the Last Glacial Maximum (LGM) and recolonization in the present, respectively, comparing to the Last Interglacial (LIG). These findings suggest that the two species extensively occurred in the Northwest of China before the Quaternary, and the current populations of them originated from a few separated glacial refugia following their habitat fragmentation in the Quarternary. Our results provide new insights on the impact of past geological and climatic fluctuations on the population dynamics of desert plants in northwestern China, and further enforce the hypothesis that there were several independent glacial refugia for these species during the Quaternary glaciations.

Climatic and soil characteristics account for the genetic structure of the invasive cactus moth Cactoblastis cactorum, in its native range in Argentina.

Knowledge of the physical and environmental conditions that may limit the migration of invasive species is crucial to assess the potential for expansion outside their native ranges. The cactus moth, Cactoblastis cactorum, is native to South America (Argentina, Paraguay, Uruguay and Brazil) and has been introduced and invaded the Caribbean and southern United States, among other regions. In North America there is an ongoing process of range expansion threatening cacti biodiversity of the genus Opuntia and the commercial profits of domesticated Opuntia ficus-indica. To further understand what influences the distribution and genetic structure of this otherwise important threat to native and managed ecosystems, in the present study we combined ecological niche modeling and population genetic analyses to identify potential environmental barriers in the native region of Argentina. Samples were collected on the host with the wider distribution range, O. ficus-indica. Significant genetic structure was detected using 10 nuclear microsatellites and 24 sampling sites. At least six genetic groups delimited by mountain ranges, salt flats and wetlands were mainly located to the west of the Dry Chaco ecoregion. Niche modeling supports that this region has high environmental suitability where the upper soil temperature and humidity, soil carbon content and precipitation were the main environmental factors that explain the presence of the moth. Environmental filters such as the upper soil layer may be critical for pupal survival and consequently for the establishment of populations in new habitats, whereas the presence of available hosts is a necessary conditions for insect survival, upper soil and climatic characteristics will determine the opportunities for a successful establishment.

The long-term survival and climatic distribution of mixotrophic and mycoheterotrophic orchids

Orchid germination depends on their fungal partner; however, there are no broadscale analyses evaluating the actual overlap between orchids and their mycorrhizal symbionts. The aim of this research was to evaluate the importance of mycorrhizal fungi for the occurrence of two species of orchids using ecological niche modeling (ENM). Two sets of future orchid distribution models were created – the first one was based on bioclimatic data only, and the second one included information about the distribution of fungal symbionts. The jackknife test indicated that for both mixotrophic and mycoheterotrophic orchids, the presence of symbiotic fungi is crucial for their occurrence, and ENM analyses revealed that both orchids face habitat loss as a result of predicted changes in climate. In the case of the mixotrophic orchid, the presence of symbiotic fungi can compensate for unfavorable climatic conditions. Problems and limitations in modeling the distributions of species are discussed in terms of the symbiotic relationship.

Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae.

Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.

Emerging threat of ranavirus: prevalence, genetic diversity, and climatic drivers of Ranavirus (Iridoviridae) in ectothermic vertebrates of Asia

IntroductionRanavirus disease, caused by viruses within the genus Ranavirus (Iridoviridae), is considered a globally emerging infectious disease linked to mass mortality events in both wild and cultured ectothermic vertebrates. Surveillance work is, however, limited in Asia hence prevalence and the dynamics of the disease remain poorly understood. To understand disease burden and the potential biotic and abiotic drivers in southern China region, we conducted a systematic surveillance of the ranavirus across Guangxi Zhuang Autonomous region (GAR).MethodsFor this, we used a multifaceted approach involving screening of amphibians and other potential hosts, diagnostic tests, phylogenetic analyses, prevalence estimation, co-infection assessments, and climatic niche analyses. Over one thousand individuals were sampled across 25 sampling sites.ResultsWe found ninety-two individuals from 18 species of ectothermic vertebrates to be infected with ranavirus. Two lineages were responsible – Rana nigromaculata ranavirus and tiger frog virus were identified using phylogenetic analysis based on the major capsid protein (MCP) gene fragment. Out of these two lineages, the presence of tiger frog virus is rare as we came across only one case. We also found evidence of a co-infection with ranavirus and Batrachochytrium dendrobatidis that can be highly detrimental to host populations; possibly the first such documentation in Asia. Our niche modelling analysis suggests that precipitation seasonality plays an important role in ranavirus prevalence in GAR – southwestern, southeastern, central and northeastern regions of GAR can be considered to be optimum habitats for ranaviruses. Infection rates in wild frog species have reached 100% in some areas, even in nature reserves.DiscussionOur research also indicates that culture facilities and pet markets are frequently infected, serving as likely vectors for the regional and global spread of ranaviruses. The knowledge generated suggests the need for systematic surveillance, stringent biosecurity measures, and control of international animal trade to prevent further transmission and protection of biodiversity and aquaculture industries across Asia.

Conservation Priorities and Demographic History of Saussurea involucrata in the Tianshan Mountains and Altai Mountains.

Rare and vulnerable endemic plants represent different evolutionary units that occur at different times, and protecting these species is a key issue in biological protection. Understanding the impact of the history of endangered plant populations on their genetic diversity helps to reveal evolutionary history and is crucial for guiding conservation efforts. Saussurea involucrata, a perennial alpine species mainly distributed in the Tianshan Mountains, is famous for its medicinal value but has become endangered due to over-exploitation. In the present study, we employed both nuclear and chloroplast DNA sequences to investigate the genetic distribution pattern and evolutionary history of S. involucrata. A total of 270 individuals covering nine S. involucrata populations were sampled for the amplification and sequencing of nrDNA Internal Transcribed Spacer (ITS) and chloroplast trnL-trnF, matK and ndhF-rpl32 sequences. Via calculation, we identified 7 nuclear and 12 plastid haplotypes. Among the nine populations, GL and BA were characterized by high haplotype diversity, whereas BG revealed the lowest haplotype diversity. Molecular dating estimations suggest that divergence among S. involucrata populations occurred around 0.75 Ma, coinciding with the uplift of Tianshan Mountains. Our results reveal that both isolation-by-distance (IBD) and isolation-by-resistance (IBR) have promoted genetic differentiation among populations of S. involucrata. The results from the ecological niche modeling analyses show a more suitable habitat for S. involucrata in the past than at present, indicating a historical distribution contraction of the species. This study provides new insight into understanding the genetic differentiation of S. involucrata, as well as the theoretical basis for conserving this species.

Phylogeny-based taxonomic revision and niche modelling of the rove beetle genus Loncovilius Germain, 1903 (Coleoptera: Staphylinidae: Staphylininae)

Abstract Using a phylogenetic analysis as a baseline, we conducted a taxonomic revision of the genus Loncovilius Germain, 1903 which now includes 10 valid species. Of them, six species, all restricted to the southern Andean region, are described as new for science: Loncovilius barclayisp. nov., L. cantharoidessp. nov., L. carlsbergisp. nov., L. hammondisp. nov., L. impunctussp. nov., and Loncovilius variabilissp. nov. A lectotype is designated for Loncovilius edwardsianus and an updated key is provided for the identification of all species of the genus. Apoquediusstat. nov. and Lienturiusstat. nov. initially described as a subgenera, are given a status of separate genera within Amblyopinini. Our phylogeny necessitated the following new combinations: Apoquedius aeneipennis, comb. nov., A. piciformis, comb. nov., Lienturius leiocephalus, comb. nov., Sphingoquedius discoideus, comb. nov. and S. brevis, comb. nov. and Sphingoquedius nanus, comb. nov. The ecological niche modeling analyses predict a substantial contraction of the local distribution range of L. cantharoides, L. edwardsianus, and L. lividipennis during the warmer periods of the future. For L. variabilis most areas are predicted to remain suitable.

Coastal-inland divergence and postglacial expansion in the populations of the orchid bee Euglossa annectans

Biogeographic patterns in the southernmost portion of the Atlantic Forest (AF) are still elusive for a high number of endemic species where the main phylogeographic hypothesis in AF (e.g., CM model or AF expansion) fails to predict refuges during the Last Glacial Maximum (LGM). Euglossa annectans is an orchid bee species endemic to AF, distributed throughout the longitudinal edges of the southern portions of this biome. Combining ecological niche modelling and genetic analysis, we investigated whether the Pleistocene climate fluctuations played some role in the population structure of this species. We analysed 640 bp of the Cytb gene and eight microsatellite loci from males sampled from twelve localities along E. annectans distribution. Microsatellite markers indicated two main groups with a disjunction between inland and coastal areas. Although mitochondrial data showed no spatial structure, we found signals of a bottleneck followed by population expansion after the LGM. Pleistocene climatic models revealed a fragmented scenario with suitable areas concentrated at the coastal continental shelf and the northern-west inland areas, both in line with the genetic nuclear markers’ structure and synchronic with the mitochondrial bottleneck at the LGM. The climatic instability along the Pleistocene has played a central role in determining the phylogeographic and demographic patterns of the E. annectans, resulting in a genetic structure reported for the first time in this area.

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout.

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.

Range shift and loss of genetic diversity under climate change in the red-backed fairywren (Malurus melanocephalus), an Australian endemic bird species

AbstractClimatic variability is the most important force influencing the distribution dynamics of common and widespread species, with significant effects on their current biogeographical patterns. In this study, phylogeography was integrated with ecological niche modelling to understand the range dynamics of an Australian bird species, the red-backed fairywren (Malurus melanocephalus), under various climate change scenarios. Specifically, an ecological niche modelling approach with Bayesian-based phylogeographical analysis was used to develop robust inferences regarding the demographic history of the species. The predictions of the model were mostly consistent with the present distribution of the species. However, under the Last Interglacial bioclimatic conditions, the model predicted a significantly narrower distribution than today, indicating the existence of allopatric refugia. Predictions for the Last Glacial Maximum indicated that the species had a wider distribution, extending northwards. Additionally, predictions for the future (2050 and 2070) indicated that the species will probably have a narrower distribution than at present, which will be shifted eastwards. The extended Bayesian skyline plot analysis, which provides a robust analysis of fluctuations in the effective population size throughout the evolutionary history of a species, produced results highly consistent with the ecological niche modelling predictions for the red-backed fairywren. This is the first study to investigate the Late Quaternary history of an endemic avian taxon from Australia using ecological niche modelling and Bayesian-based demographic analysis.

Distributional Response of the Rare and Endangered Tree Species Abies chensiensis to Climate Change in East Asia.

Globally, increasing temperatures due to climate change have severely affected natural ecosystems in several regions of the world; however, the impact on the alpine plant may be particularly profound, further raising the risk of extinction for rare and endangered alpine plants. To identify how alpine species have responded to past climate change and to predict the potential geographic distribution of species under future climate change, we investigated the distribution records of A. chensiensis, an endangered alpine plant in the Qinling Mountains listed in the Red List. In this study, the optimized MaxEnt model was used to analyse the key environmental variables related to the distribution of A. chensiensis based on 93 wild distribution records and six environmental variables. The potential distribution areas of A. chensiensis in the last interglacial (LIG), the last glacial maximum (LGM), the current period, and the 2050s and 2070s were simulated. Our results showed that temperature is critical to the distribution of A. chensiensis, with the mean temperature of the coldest quarter being the most important climatic factor affecting the distribution of this species. In addition, ecological niche modeling analysis showed that the A. chensiensis distribution area in the last interglacial experiencing population expansion and, during the last glacial maximum occurring, a population contraction. Under the emission scenarios in the 2050s and 2070s, the suitable distribution area would contract significantly, and the migration routes of the centroids tended to migrate toward the southern high-altitude mountains, suggesting a strong response from the A. chensiensis distribution to climate change. Collectively, the results of this study provide a comprehensive and multidimensional perspective on the geographic distribution pattern and history of population dynamics for the endemic, rare, and endangered species, A. chensiensis, and it underscores the significant impact of geological and climatic changes on the geographic pattern of alpine species populations.

Molecular, morphometric, and spatial data analyses provide new insights into the evolutionary history of the Peromyscus boylii species complex (Rodentia: Cricetidae) in the mountains of Mexico

Peromyscus is the most speciose genus in America, which occupies almost every terrestrial habitat type. However, its taxonomy and evolutionary relationships remain unsolved in several species, one species group with these issues is the P. boylii complex. This complex consists of 11 species (P. beatae, P. boylii, P. carletoni, P. ensinki, P. greenbaumi, P. kilpatricki, P. levipes, P. madrensis, P. schmidlyi, P. simulus, and P. stephani) largely distributed in Mexico and has been taxonomically studied during the last 40 years, resulting in the description of new species, several of them from the mountains of central Mexico. In this study, we aimed to integrate molecular, morphometric, and spatial data analysis approaches to inquire into the phylogenetic relationships. To clarify the taxonomic status of the P. boylii complex, particularly for the species distributed in the central Mexican highlands where the taxonomic uncertainty is high. We performed phylogenetic and divergence time analyses based on four molecular markers for all species within the complex, we explored cranium shape and size variation in 146 individuals of continental species (P. madrensis and P. stephani excluded) using geometric morphometrics. Also, we evaluated environmental differentiation and ecological niche modeling analyses of three species endemic to the central Mexican highlands to retrieve evidence on their evolutionary history. Our results recovered one well-supported clade including all mountainous species, in which P. schmidlyi was sister to the clade composed of P. greenbaumi and P. ensinki, which diverged during the late Pleistocene. The novel morphological data allowed a better differentiation of all continental species. The discovery of new specimens for P. greenbaumi and P. ensinki improved their taxonomic knowledge, as well as delimiting their habitat and distribution, showing substantial environmental divergence with low overlapped geographical distributions; P. schmidlyi restricted to the Sierra Madre Occidental, P. ensinki to the central-west Trans-Mexican Volcanic Belt, and P. greenbaumi to the center of the Sierra Madre del Sur. We discuss the biogeographic history of these three lineages and the role of the late Pleistocene climatic oscillations on their diversification.